<commit_before><tool id="transdecoder" name="TransDecoder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>finds coding regions within transcripts</description>
    <xrefs>
        <xref type="bio.tools">TransDecoder</xref>
    </xrefs>
    <macros>
        <token name="@TOOL_VERSION@">5.5.0</token>
        <token name="@VERSION_SUFFIX@">1</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">transdecoder</requirement>
        <requirement type="package" version="3.0">zip</requirement>
    </requirements>
    <version_command><![CDATA[TransDecoder.LongOrfs --version 2>&1 | grep 'TransDecoder.LongOrfs' | cut -f 2 -d ' ']]></version_command>
    <command detect_errors="exit_code"><![CDATA[
## initialize
ln -s '${t}' 'transcripts.fasta' &&

## run TransDecoder.LongOrfs
TransDecoder.LongOrfs
## Shared options
-t 'transcripts.fasta'
-G '${G}'
## LongOrfs options
#if $lo.gene_trans_map
    --gene_trans_map '${lo.gene_trans_map}'
#end if
-m $lo.m
${lo.S}
-O 'output' ## required, otherwise value of -t is used as output folder

## run TransDecoder.Predict
#if $po.predict_cond.predict_sel == 'yes'
    && TransDecoder.Predict
    ## Shared options
    -t 'transcripts.fasta'
    -G '${G}'
    ## Predict options
    --retain_long_orfs_mode $po.predict_cond.mode_cond.mode_sel
    #if $po.predict_cond.mode_cond.mode_sel == 'strict'
        --retain_long_orfs_length $po.predict_cond.mode_cond.retain_long_orfs_length
    #end if
    #if $po.predict_cond.retain_pfam_hits
        --retain_pfam_hits '$po.predict_cond.retain_pfam_hits'
    #end if
    #if $po.predict_cond.retain_blastp_hits
        --retain_blastp_hits '$po.predict_cond.retain_blastp_hits'
    #end if
    $po.predict_cond.single_best_only
    $po.predict_cond.no_refine_starts
    -T $po.predict_cond.T
    -O 'output'
#end if

## postprocessing
#if 'log' in $oo.out
    |& tee '$out_log'
#end if
&& if ls 'output/'*'.pdf' >/dev/null 2>&1; then zip 'seqlogo.zip' 'output/'*'.pdf' -q -j; fi
    ]]></command>
    <inputs>
        <param argument="-t" type="data" format="fasta" label="Select file with transcripts"/>
        <param argument="-G" type="select" label="Select genetic code">
            <option value="Acetabularia">Acetabularia</option>
            <option value="Candida">Candida</option>
            <option value="Ciliate">Ciliate</option>
            <option value="Dasycladacean">Dasycladacean</option>
            <option value="Euplotid">Euplotid</option>
            <option value="Hexamita">Hexamita</option>
            <option value="Mesodinium">Mesodinium</option>
            <option value="Mitochondrial-Ascidian">Mitochondrial-Ascidian</option>
            <option value="Mitochondrial-Chlorophycean">Mitochondrial-Chlorophycean</option>
            <option value="Mitochondrial-Echinoderm">Mitochondrial-Echinoderm</option>
            <option value="Mitochondrial-Flatworm">Mitochondrial-Flatworm</option>
            <option value="Mitochondrial-Invertebrates">Mitochondrial-Invertebrates</option>
            <option value="Mitochondrial-Protozoan">Mitochondrial-Protozoan</option>
            <option value="Mitochondrial-Pterobranchia">Mitochondrial-Pterobranchia</option>
            <option value="Mitochondrial-Scenedesmus_obliquus">Mitochondrial-Scenedesmus_obliquus</option>
            <option value="Mitochondrial-Thraustochytrium">Mitochondrial-Thraustochytrium</option>
            <option value="Mitochondrial-Trematode">Mitochondrial-Trematode</option>
            <option value="Mitochondrial-Vertebrates">Mitochondrial-Vertebrates</option>
            <option value="Mitochondrial-Yeast">Mitochondrial-Yeast</option>
            <option value="Pachysolen_tannophilus">Pachysolen_tannophilus</option>
            <option value="Peritrich">Peritrich</option>
            <option value="SR1_Gracilibacteria">SR1_Gracilibacteria</option>
            <option value="Tetrahymena">Tetrahymena</option>
            <option value="Universal" selected="true">Universal</option>
        </param>
        <section name="lo" title="LongOrfs options" expanded="true">
            <param argument="--gene_trans_map" type="data" format="tabular" optional="true" label="Select gene-to-transcript identifier mapping file" help="gene_id&lt;tab&gt;trans_id&lt;return&gt;"/>
            <param argument="-m" type="integer" value="100" min="1" label="Set minimum protein length"/>
            <param argument="-S" type="boolean" truevalue="-S" falsevalue="" label="Activate strand-specificity?" help="Only analyse top strand?"/>
        </section>
        <section name="po" title="Predict options" expanded="true">
            <!-- 
                TransDecoder.Predict can be skipped if only longest_orfs.pep (as a result of TransDecoder.LongOrfs) is required, e.g. for homology search via BlastP and Pfam.
            -->
            <conditional name="predict_cond">
                <param name="predict_sel" type="select" label="Should likely coding regions be predicted?" help="(TransDecoder.Predict)">
                    <option value="yes" selected="true">Yes</option>
                    <option value="no">No</option>
                </param>
                <when value="yes">
                    <conditional name="mode_cond">
                        <param argument="mode_sel" type="select" label="Select mode to retain long ORFs" help="In dynamic mode: set range according to 1% FDR in a random sequence of same GC content.">
                            <option value="dynamic" selected="true">Dynamic</option>
                            <option value="strict">Strict</option>
                        </param>
                        <when value="dynamic"/>
                        <when value="strict">
                            <param argument="--retain_long_orfs_length" type="integer" value="1000000" min="0" label="Set long ORFs length" help="Retain all ORFs found that are equal or longer than these many nucleotides even if no other evidence marks it as coding."/>
                        </when>
                    </conditional>
                    <param argument="--retain_blastp_hits" type="data" format="tabular" optional="true" label="Select BlastP result file" help="Any ORF with a blast match will be retained in the final output. (tabular outfmt6 file)"/>
                    <param argument="--retain_pfam_hits" type="data" format="tabular" optional="true" label="Select Pfam result file" help="Domain table output file from running hmmscan to search Pfam. Any ORF with a pfam domain hit will be retained in the final output. (tabular domtblout file)"/>
                    <param argument="--single_best_only" type="boolean" truevalue="--single_best_only" falsevalue="" label="Retain only the single best ORF per transcript?" help="Prioritized by homology than ORF length."/>
                    <param argument="--no_refine_starts" type="boolean" truevalue="--no_refine_starts" falsevalue="" label="Start refinement that identifies potential start codons for 5' partial ORFs using a PWM?"/>
                    <param argument="-T" type="integer" value="500" min="1" label="Set top longest ORFs to train Markov Model" help="The first (10*value) elements are selected for removing redundancies. Then number of longst ORFs of this value are selected from the non-redundant set."/>
                </when>
                <when value="no"/>
            </conditional>
        </section>
        <section name="oo" title="Output options" expanded="true">
            <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)" help="Only shown in history if selected here and generated by the specific run.">
                <!-- LongOrfs -->
                <option value="lo_cds">Longest ORFs (CDS)</option>
                <option value="lo_gff3">Longest ORFs (GFF3)</option>
                <option value="lo_pep" selected="true">Longest ORFs (PEP)</option>
                <!-- Predict -->
                <option value="bed" selected="true">Results (BED)</option><commit_msg>transdecoder: domtbl input from hmmscan needs to be txt (#4067)<commit_after><tool id="transdecoder" name="TransDecoder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
    <description>finds coding regions within transcripts</description>
    <xrefs>
        <xref type="bio.tools">TransDecoder</xref>
    </xrefs>
    <macros>
        <token name="@TOOL_VERSION@">5.5.0</token>
        <token name="@VERSION_SUFFIX@">2</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">transdecoder</requirement>
        <requirement type="package" version="3.0">zip</requirement>
    </requirements>
    <version_command><![CDATA[TransDecoder.LongOrfs --version 2>&1 | grep 'TransDecoder.LongOrfs' | cut -f 2 -d ' ']]></version_command>
    <command detect_errors="exit_code"><![CDATA[
## initialize
ln -s '${t}' 'transcripts.fasta' &&

## run TransDecoder.LongOrfs
TransDecoder.LongOrfs
## Shared options
-t 'transcripts.fasta'
-G '${G}'
## LongOrfs options
#if $lo.gene_trans_map
    --gene_trans_map '${lo.gene_trans_map}'
#end if
-m $lo.m
${lo.S}
-O 'output' ## required, otherwise value of -t is used as output folder

## run TransDecoder.Predict
#if $po.predict_cond.predict_sel == 'yes'
    && TransDecoder.Predict
    ## Shared options
    -t 'transcripts.fasta'
    -G '${G}'
    ## Predict options
    --retain_long_orfs_mode $po.predict_cond.mode_cond.mode_sel
    #if $po.predict_cond.mode_cond.mode_sel == 'strict'
        --retain_long_orfs_length $po.predict_cond.mode_cond.retain_long_orfs_length
    #end if
    #if $po.predict_cond.retain_pfam_hits
        --retain_pfam_hits '$po.predict_cond.retain_pfam_hits'
    #end if
    #if $po.predict_cond.retain_blastp_hits
        --retain_blastp_hits '$po.predict_cond.retain_blastp_hits'
    #end if
    $po.predict_cond.single_best_only
    $po.predict_cond.no_refine_starts
    -T $po.predict_cond.T
    -O 'output'
#end if

## postprocessing
#if 'log' in $oo.out
    |& tee '$out_log'
#end if
&& if ls 'output/'*'.pdf' >/dev/null 2>&1; then zip 'seqlogo.zip' 'output/'*'.pdf' -q -j; fi
    ]]></command>
    <inputs>
        <param argument="-t" type="data" format="fasta" label="Select file with transcripts"/>
        <param argument="-G" type="select" label="Select genetic code">
            <option value="Acetabularia">Acetabularia</option>
            <option value="Candida">Candida</option>
            <option value="Ciliate">Ciliate</option>
            <option value="Dasycladacean">Dasycladacean</option>
            <option value="Euplotid">Euplotid</option>
            <option value="Hexamita">Hexamita</option>
            <option value="Mesodinium">Mesodinium</option>
            <option value="Mitochondrial-Ascidian">Mitochondrial-Ascidian</option>
            <option value="Mitochondrial-Chlorophycean">Mitochondrial-Chlorophycean</option>
            <option value="Mitochondrial-Echinoderm">Mitochondrial-Echinoderm</option>
            <option value="Mitochondrial-Flatworm">Mitochondrial-Flatworm</option>
            <option value="Mitochondrial-Invertebrates">Mitochondrial-Invertebrates</option>
            <option value="Mitochondrial-Protozoan">Mitochondrial-Protozoan</option>
            <option value="Mitochondrial-Pterobranchia">Mitochondrial-Pterobranchia</option>
            <option value="Mitochondrial-Scenedesmus_obliquus">Mitochondrial-Scenedesmus_obliquus</option>
            <option value="Mitochondrial-Thraustochytrium">Mitochondrial-Thraustochytrium</option>
            <option value="Mitochondrial-Trematode">Mitochondrial-Trematode</option>
            <option value="Mitochondrial-Vertebrates">Mitochondrial-Vertebrates</option>
            <option value="Mitochondrial-Yeast">Mitochondrial-Yeast</option>
            <option value="Pachysolen_tannophilus">Pachysolen_tannophilus</option>
            <option value="Peritrich">Peritrich</option>
            <option value="SR1_Gracilibacteria">SR1_Gracilibacteria</option>
            <option value="Tetrahymena">Tetrahymena</option>
            <option value="Universal" selected="true">Universal</option>
        </param>
        <section name="lo" title="LongOrfs options" expanded="true">
            <param argument="--gene_trans_map" type="data" format="tabular" optional="true" label="Select gene-to-transcript identifier mapping file" help="gene_id&lt;tab&gt;trans_id&lt;return&gt;"/>
            <param argument="-m" type="integer" value="100" min="1" label="Set minimum protein length"/>
            <param argument="-S" type="boolean" truevalue="-S" falsevalue="" label="Activate strand-specificity?" help="Only analyse top strand?"/>
        </section>
        <section name="po" title="Predict options" expanded="true">
            <!-- 
                TransDecoder.Predict can be skipped if only longest_orfs.pep (as a result of TransDecoder.LongOrfs) is required, e.g. for homology search via BlastP and Pfam.
            -->
            <conditional name="predict_cond">
                <param name="predict_sel" type="select" label="Should likely coding regions be predicted?" help="(TransDecoder.Predict)">
                    <option value="yes" selected="true">Yes</option>
                    <option value="no">No</option>
                </param>
                <when value="yes">
                    <conditional name="mode_cond">
                        <param argument="mode_sel" type="select" label="Select mode to retain long ORFs" help="In dynamic mode: set range according to 1% FDR in a random sequence of same GC content.">
                            <option value="dynamic" selected="true">Dynamic</option>
                            <option value="strict">Strict</option>
                        </param>
                        <when value="dynamic"/>
                        <when value="strict">
                            <param argument="--retain_long_orfs_length" type="integer" value="1000000" min="0" label="Set long ORFs length" help="Retain all ORFs found that are equal or longer than these many nucleotides even if no other evidence marks it as coding."/>
                        </when>
                    </conditional>
                    <param argument="--retain_blastp_hits" type="data" format="tabular" optional="true" label="Select BlastP result file" help="Any ORF with a blast match will be retained in the final output. (tabular outfmt6 file)"/>
                    <param argument="--retain_pfam_hits" type="data" format="txt" optional="true" label="Select Pfam result file" help="Domain table output file from running hmmscan to search Pfam. Any ORF with a pfam domain hit will be retained in the final output. (tabular domtblout file)"/>
                    <param argument="--single_best_only" type="boolean" truevalue="--single_best_only" falsevalue="" label="Retain only the single best ORF per transcript?" help="Prioritized by homology than ORF length."/>
                    <param argument="--no_refine_starts" type="boolean" truevalue="--no_refine_starts" falsevalue="" label="Start refinement that identifies potential start codons for 5' partial ORFs using a PWM?"/>
                    <param argument="-T" type="integer" value="500" min="1" label="Set top longest ORFs to train Markov Model" help="The first (10*value) elements are selected for removing redundancies. Then number of longst ORFs of this value are selected from the non-redundant set."/>
                </when>
                <when value="no"/>
            </conditional>
        </section>
        <section name="oo" title="Output options" expanded="true">
            <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)" help="Only shown in history if selected here and generated by the specific run.">
                <!-- LongOrfs -->
                <option value="lo_cds">Longest ORFs (CDS)</option>
                <option value="lo_gff3">Longest ORFs (GFF3)</option>
                <option value="lo_pep" selected="true">Longest ORFs (PEP)</option>
                <!-- Predict -->
                <option value="bed" selected="true">Results (BED)</option>
{'fraction_non_alphanumeric': 0.13167259786476868, 'fraction_numerical': 0.004908577739599951, 'mean_word_length': 3.072713643178411, 'pattern_counts': {'":': 0, '<': 253, '<?xml version=': 0, '>': 259, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '5377982', 'n_tokens_mistral': 5079, 'n_tokens_neox': 4700, 'n_words': 1101}