<commit_before><tool id="deseq2" name="DESeq2" version="2.1.8.0">
    <description>Determines differentially expressed features from count tables</description>
    <requirements>
        <!-- odering is crucial, otherwise R will override the ENV variables from deseq2 -->
        <requirement type="package" version="3.2.1">R</requirement>
        <requirement type="package" version="3.10.2">atlas</requirement>
        <requirement type="package" version="1.8.1">deseq2</requirement>
    </requirements>
    <version_command>
    <![CDATA[
        echo $(R --version | grep version | grep -v GNU)", DESeq2 version" $(R --vanilla --slave -e "library(DESeq2) ;
        cat(sessionInfo()\$otherPkgs\$DESeq2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
    ]]>
    </version_command>
    <command interpreter="Rscript">
    <![CDATA[
        #import json
        \$DESEQ2_ROOT_PATH/inst/script/deseq2.R
            -o "$deseq_out"
            #if $pdf:
                -p "$plots"
            #end if
            #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
                $temp_factor_names.append([str($factor.factorName), $temp_factor])
            #end for<commit_msg>fix script path<commit_after><tool id="deseq2" name="DESeq2" version="2.1.8.0">
    <description>Determines differentially expressed features from count tables</description>
    <requirements>
        <!-- odering is crucial, otherwise R will override the ENV variables from deseq2 -->
        <requirement type="package" version="3.2.1">R</requirement>
        <requirement type="package" version="3.10.2">atlas</requirement>
        <requirement type="package" version="1.8.1">deseq2</requirement>
    </requirements>
    <version_command>
    <![CDATA[
        echo $(R --version | grep version | grep -v GNU)", DESeq2 version" $(R --vanilla --slave -e "library(DESeq2) ;
        cat(sessionInfo()\$otherPkgs\$DESeq2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
    ]]>
    </version_command>
    <command interpreter="Rscript">
    <![CDATA[
        #import json
        \$DESEQ2_ROOT_PATH/script/deseq2.R
            -o "$deseq_out"
            #if $pdf:
                -p "$plots"
            #end if
            #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
                $temp_factor_names.append([str($factor.factorName), $temp_factor])
            #end for
{'fraction_non_alphanumeric': 0.13723038449515473, 'fraction_numerical': 0.015004688965301657, 'mean_word_length': 2.0651340996168583, 'pattern_counts': {'":': 0, '<': 37, '<?xml version=': 0, '>': 37, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 2, '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': '3360088', 'n_tokens_mistral': 987, 'n_tokens_neox': 930, 'n_words': 213}