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comparison multiqc.xml @ 6:01237d721a9f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361
author iuc
date Sat, 23 Dec 2017 15:57:55 -0500
parents 5746cb5cf08d
children 467486f1c568
comparison
equal deleted inserted replaced
5:5746cb5cf08d 6:01237d721a9f
1 <tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@.1"> 1 <tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@.1">
2 <description>aggregate results from bioinformatics analyses into a single report</description> 2 <description>aggregate results from bioinformatics analyses into a single report</description>
3 <macros> 3 <macros>
4 <token name="@WRAPPER_VERSION@">1.2</token> 4 <token name="@WRAPPER_VERSION@">1.3</token>
5 <token name="@LN_FILES@"> 5 <token name="@LN_FILES@">
6 <![CDATA[ 6 <![CDATA[
7 #for $file in $repeat.software_cond.input 7 #for $file in $repeat.software_cond.input
8 grep -q "$pattern" $file || die "'$pattern' not found in the file" && 8 grep -q "$pattern" $file || die "'$pattern' not found in the file" &&
9 ln -s '$file' '$software_dir/${file.element_identifier}' && 9 ln -s '$file' '$software_dir/${file.element_identifier}' &&
131 #for $file in $repeat.software_cond.input 131 #for $file in $repeat.software_cond.input
132 ln -s '${file}' '$software_dir/HiCUP_summary_report_${file.element_identifier}' && 132 ln -s '${file}' '$software_dir/HiCUP_summary_report_${file.element_identifier}' &&
133 #end for 133 #end for
134 #elif str($repeat.software_cond.software) == "hisat2" 134 #elif str($repeat.software_cond.software) == "hisat2"
135 #set $pattern = "HISAT2 summary stats:" 135 #set $pattern = "HISAT2 summary stats:"
136 @LN_FILES@
137 #elif str($repeat.software_cond.software) == "hicexplorer"
138 #set $pattern = "Min rest. site distance"
136 @LN_FILES@ 139 @LN_FILES@
137 #elif str($repeat.software_cond.software) == "htseq" 140 #elif str($repeat.software_cond.software) == "htseq"
138 #set $pattern = "__too_low_aQual" 141 #set $pattern = "__too_low_aQual"
139 @LN_FILES@ 142 @LN_FILES@
140 #elif str($repeat.software_cond.software) == "kallisto" 143 #elif str($repeat.software_cond.software) == "kallisto"
380 <option value="fastqc">FastQC</option> 383 <option value="fastqc">FastQC</option>
381 <option value="featureCounts">featureCounts</option> 384 <option value="featureCounts">featureCounts</option>
382 <option value="flexbar">Flexbar</option> 385 <option value="flexbar">Flexbar</option>
383 <option value="gatk">GATK (BaseRecalibrator or VariantEval output)</option> 386 <option value="gatk">GATK (BaseRecalibrator or VariantEval output)</option>
384 <!--<option value="goleft_indexcov">goleft indexcov</option>--> 387 <!--<option value="goleft_indexcov">goleft indexcov</option>-->
388 <option value="hicexplorer">HiCExplorer</option>
385 <!--<option value="hicup">HiCUP</option>--> 389 <!--<option value="hicup">HiCUP</option>-->
386 <option value="hisat2">HISAT2</option> 390 <option value="hisat2">HISAT2</option>
387 <!--<option value="homer">HOMER</option>--> 391 <!--<option value="homer">HOMER</option>-->
388 <option value="htseq">HTSeq</option> 392 <option value="htseq">HTSeq</option>
389 <!--<option value="jellyfish">Jellyfish</option>--> 393 <!--<option value="jellyfish">Jellyfish</option>-->
465 <option value="base_recalibrator">Base recalibrator file</option> 469 <option value="base_recalibrator">Base recalibrator file</option>
466 </param> 470 </param>
467 <param name="input" type="data" format="txt" multiple="true" label="GATK output"/> 471 <param name="input" type="data" format="txt" multiple="true" label="GATK output"/>
468 </repeat> 472 </repeat>
469 </when> 473 </when>
474 <when value="hicexplorer">
475 <param name="input" type="data" format="txt,tabular" multiple="true" label="Output of HiCExplorer" help="It should contain 'Min rest. site distance'"/>
476 </when>
470 <when value="hisat2"> 477 <when value="hisat2">
471 <param name="input" type="data" format="txt,tabular" multiple="true" label="Output of HISAT2" help="It should contain 'HISAT2 summary stats:'"/> 478 <param name="input" type="data" format="txt,tabular" multiple="true" label="Output of HISAT2" help="It should contain 'HISAT2 summary stats:'"/>
472 </when> 479 </when>
473 <when value="htseq"> 480 <when value="htseq">
474 <param name="input" type="data" format="txt,tabular" multiple="true" label="Output of HTSeq" help="It should contain '__too_low_aQual'"/> 481 <param name="input" type="data" format="txt,tabular" multiple="true" label="Output of HTSeq" help="It should contain '__too_low_aQual'"/>
725 <param name="input" value="hisat2_1.txt,hisat2_2.txt" /> 732 <param name="input" value="hisat2_1.txt,hisat2_2.txt" />
726 </conditional> 733 </conditional>
727 </repeat> 734 </repeat>
728 <repeat name="results"> 735 <repeat name="results">
729 <conditional name="software_cond"> 736 <conditional name="software_cond">
737 <param name="software" value="hicexplorer" />
738 <param name="input" value="hicexplorer1.log,hicexplorer2.log" />
739 </conditional>
740 </repeat>
741 <repeat name="results">
742 <conditional name="software_cond">
730 <param name="software" value="kallisto" /> 743 <param name="software" value="kallisto" />
731 <param name="input" value="kallisto_1.txt,kallisto_2.txt" /> 744 <param name="input" value="kallisto_1.txt,kallisto_2.txt" />
732 </conditional> 745 </conditional>
733 </repeat> 746 </repeat>
734 <repeat name="results"> 747 <repeat name="results">
761 <has_text text="bowtie2_se_plot" /> 774 <has_text text="bowtie2_se_plot" />
762 <has_text text="hisat2_se_plot" /> 775 <has_text text="hisat2_se_plot" />
763 <has_text text="kallisto_alignment" /> 776 <has_text text="kallisto_alignment" />
764 <has_text text="star_alignment_plot" /> 777 <has_text text="star_alignment_plot" />
765 <has_text text="tophat_alignment" /> 778 <has_text text="tophat_alignment" />
779 <has_text text="hicexplorer" />
780
766 </assert_contents> 781 </assert_contents>
767 </output> 782 </output>
768 <output_collection name="stats" type="list"> 783 <output_collection name="stats" type="list">
769 <element name="bismark_alignment" file="bismark_stats.tabular" compare="sim_size" delta="10"/> 784 <element name="bismark_alignment" file="bismark_stats.tabular" compare="sim_size" delta="10"/>
770 <element name="bowtie2" file="bowtie2_stats.tabular" compare="sim_size" delta="0"/> 785 <element name="bowtie2" file="bowtie2_stats.tabular" compare="sim_size" delta="0"/>
771 <element name="general_stats" file="aligner_soft_stats.tabular" compare="sim_size" delta="50"/> 786 <element name="general_stats" file="aligner_soft_stats.tabular" compare="sim_size" delta="50"/>
772 <element name="hisat2" file="hisat2_stats.tabular" compare="sim_size" delta="0"/> 787 <element name="hisat2" file="hisat2_stats.tabular" compare="sim_size" delta="0"/>
788 <!-- <element name="hicexplorer" file="hicexplorer_stats.tabular" compare="sim_size" delta="0"/> -->
773 <element name="kallisto" file="kallisto_stats.tabular" compare="sim_size" delta="10"/> 789 <element name="kallisto" file="kallisto_stats.tabular" compare="sim_size" delta="10"/>
774 <element name="star" file="star_stats.tabular" compare="sim_size" delta="10"/> 790 <element name="star" file="star_stats.tabular" compare="sim_size" delta="10"/>
775 <element name="tophat.txt" file="tophat_stats.tabular" compare="sim_size" delta="10"/> 791 <element name="tophat.txt" file="tophat_stats.tabular" compare="sim_size" delta="10"/>
776 </output_collection> 792 </output_collection>
777 </test> 793 </test>