<commit_before><tool id="dexseq" name="DEXSeq" version="1.0">
    <description>Determines differential exon usage from count tables</description>
    <requirements>
        <requirement type="package" version="1.14">dexseq</requirement>
    </requirements>
    <code file="dexseq_helper.py" />
    <stdio>
        <regex match="Execution halted" 
           source="both" 
           level="fatal" 
           description="Execution halted." />
        <regex match="Input-Error 01" 
           source="both" 
           level="fatal" 
           description="Error in your input parameters: Make sure you only apply factors to selected samples." />
        <regex match="Error in"
           source="both"
           level="fatal"
           description="An undefined error occured, please check your input carefully and contact your administrator." />
        <regex match="Error:"
            source="both"
            level="fatal"
            description="Error in the R script." />
    </stdio>
    <command>
    <![CDATA[
        mkdir ./html_out &&
        #import json
        Rscript $__tool_directory__/dexseq.R
            -o "$dexseq_out"
            -p \${GALAXY_SLOTS:-4}
            #set $temp_factor_names = list()
            #for $factor in $rep_factorName:
                #set $temp_factor = list()
                #for $level in $factor.rep_factorLevel:
                    #set $count_files = list()
                    #for $file in $level.countsFile:
                        $count_files.append(str($file))
                    #end for
                    $temp_factor.append( {str($level.factorLevel): $count_files} )
                #end for<commit_msg>Added a version command to DEXSeq wrapper<commit_after><tool id="dexseq" name="DEXSeq" version="1.0">
    <description>Determines differential exon usage from count tables</description>
    <requirements>
        <requirement type="package" version="1.14">dexseq</requirement>
    </requirements>
    <code file="dexseq_helper.py" />
    <stdio>
        <regex match="Execution halted" 
           source="both" 
           level="fatal" 
           description="Execution halted." />
        <regex match="Input-Error 01" 
           source="both" 
           level="fatal" 
           description="Error in your input parameters: Make sure you only apply factors to selected samples." />
        <regex match="Error in"
           source="both"
           level="fatal"
           description="An undefined error occured, please check your input carefully and contact your administrator." />
        <regex match="Error:"
            source="both"
            level="fatal"
            description="Error in the R script." />
    </stdio>
    <version_command>
    <![CDATA[
        echo $(R --version | grep version | grep -v GNU)", DEXSeq version" $(R --vanilla --slave -e "library(DEXSeq); cat(sessionInfo()\$otherPkgs\$DEXSeq\$Version)" 2> /dev/null | grep -v -i "WARNING: ")" (depends on DESeq2 "$(R --vanilla --slave -e "library(DESeq2); cat(sessionInfo()\$otherPkgs\$DESeq2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")")"
    ]]>
    </version_command>
    <command>
    <![CDATA[
        mkdir ./html_out &&
        #import json
        Rscript $__tool_directory__/dexseq.R
            -o "$dexseq_out"
            -p \${GALAXY_SLOTS:-4}
            #set $temp_factor_names = list()
            #for $factor in $rep_factorName:
                #set $temp_factor = list()
                #for $level in $factor.rep_factorLevel:
                    #set $count_files = list()
                    #for $file in $level.countsFile:
                        $count_files.append(str($file))
                    #end for
                    $temp_factor.append( {str($level.factorLevel): $count_files} )
                #end for
{'fraction_non_alphanumeric': 0.12506554798112218, 'fraction_numerical': 0.00550603041426324, 'mean_word_length': 1.9665629860031104, 'pattern_counts': {'":': 0, '<': 38, '<?xml version=': 0, '>': 38, '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': '3676280', 'n_tokens_mistral': 1101, 'n_tokens_neox': 1022, 'n_words': 273}