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comparison multiqc.xml @ 11:46d7ad9aa59f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
author iuc
date Mon, 06 Aug 2018 10:41:37 -0400
parents b0ce3f403e30
children a7e3e7e1019c
comparison
equal deleted inserted replaced
10:b0ce3f403e30 11:46d7ad9aa59f
1 <tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@.1"> 1 <tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@.2">
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@">1.5</token> 4 <token name="@WRAPPER_VERSION@">1.5</token>
5 <token name="@ESCAPE_IDENTIFIER@"> 5 <token name="@ESCAPE_IDENTIFIER@">
6 <![CDATA[ 6 <![CDATA[
214 #set $pattern = "__too_low_aQual" 214 #set $pattern = "__too_low_aQual"
215 @LN_FILES@ 215 @LN_FILES@
216 #elif str($repeat.software_cond.software) == "kallisto" 216 #elif str($repeat.software_cond.software) == "kallisto"
217 #set $pattern = "finding pseudoalignments for the reads" 217 #set $pattern = "finding pseudoalignments for the reads"
218 @LN_FILES@ 218 @LN_FILES@
219 #elif str($repeat.software_cond.software) == "macs2"
220 #set $pattern = "# This file is generated by MACS"
221 #for $file in $repeat.software_cond.input
222 @ESCAPE_IDENTIFIER@
223 #set file_path = os.path.join($software_dir, str($identifier) + '_peaks.xls')
224 grep -q "$pattern" $file || die "'$pattern' not found in the file" &&
225 ln -s '$file' '$file_path' &&
226 #end for
219 #elif str($repeat.software_cond.software) == "picard" 227 #elif str($repeat.software_cond.software) == "picard"
220 #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) 228 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
221 #if str($repeat2.type) == "alignment_metrics" 229 #if str($repeat2.type) == "alignment_metrics"
222 #set $pattern = "picard.analysis.AlignmentSummaryMetrics" 230 #set $pattern = "picard.analysis.AlignmentSummaryMetrics"
223 @LN_2_FILES@ 231 @LN_2_FILES@
503 <option value="htseq">HTSeq</option> 511 <option value="htseq">HTSeq</option>
504 <!--<option value="interop">InterOp</option>--> 512 <!--<option value="interop">InterOp</option>-->
505 <!--<option value="jellyfish">Jellyfish</option>--> 513 <!--<option value="jellyfish">Jellyfish</option>-->
506 <option value="kallisto">Kallisto</option> 514 <option value="kallisto">Kallisto</option>
507 <!--<option value="leehom">leeHom</option>--> 515 <!--<option value="leehom">leeHom</option>-->
508 <!--<option value="macs2">MACS2</option>--> 516 <option value="macs2">MACS2</option>
509 <!--<option value="methylQA">methylQA</option>--> 517 <!--<option value="methylQA">methylQA</option>-->
510 <!--<option value="peddy">Peddy</option>--> 518 <!--<option value="peddy">Peddy</option>-->
511 <option value="picard">Picard</option> 519 <option value="picard">Picard</option>
512 <!--<option value="preseq">Preseq</option>--> 520 <!--<option value="preseq">Preseq</option>-->
513 <option value="prokka">Prokka</option> 521 <option value="prokka">Prokka</option>
612 <param name="input" type="data" format="txt,tabular" multiple="true" label="Output of HTSeq" help="It should contain '__too_low_aQual'"/> 620 <param name="input" type="data" format="txt,tabular" multiple="true" label="Output of HTSeq" help="It should contain '__too_low_aQual'"/>
613 </when> 621 </when>
614 <when value="kallisto"> 622 <when value="kallisto">
615 <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of Kallisto" help="It should contain '[quant] finding pseudoalignments for the reads'"/> 623 <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of Kallisto" help="It should contain '[quant] finding pseudoalignments for the reads'"/>
616 </when> 624 </when>
625 <when value="macs2">
626 <param name="input" type="data" format="txt,tabular,tsv" multiple="true" label="Output of MACS2" help="It should be a tabular file containing '# This file is generated by MACS'"/>
627 </when>
617 <when value="picard"> 628 <when value="picard">
618 <repeat name="output" title="Picard output" min="1"> 629 <repeat name="output" title="Picard output" min="1">
619 <param name="type" type="select" label="Type of Picard output?"> 630 <param name="type" type="select" label="Type of Picard output?">
620 <option value="alignment_metrics">Alignment metrics</option> 631 <option value="alignment_metrics">Alignment metrics</option>
621 <option value="basedistributionbycycle">Base distribution by cycle</option> 632 <option value="basedistributionbycycle">Base distribution by cycle</option>
885 <param name="input" value="kallisto_1.txt,kallisto_2.txt" /> 896 <param name="input" value="kallisto_1.txt,kallisto_2.txt" />
886 </conditional> 897 </conditional>
887 </repeat> 898 </repeat>
888 <repeat name="results"> 899 <repeat name="results">
889 <conditional name="software_cond"> 900 <conditional name="software_cond">
901 <param name="software" value="macs2" />
902 <param name="input" value="macs_1.txt,macs_2.txt" />
903 </conditional>
904 </repeat>
905 <repeat name="results">
906 <conditional name="software_cond">
890 <param name="software" value="star" /> 907 <param name="software" value="star" />
891 <repeat name="output"> 908 <repeat name="output">
892 <conditional name="type"> 909 <conditional name="type">
893 <param name="type" value="log"/> 910 <param name="type" value="log"/>
894 <param name="input" value="star_log.txt" /> 911 <param name="input" value="star_log.txt" />
913 <assert_contents> 930 <assert_contents>
914 <has_text text="bismark-alignment" /> 931 <has_text text="bismark-alignment" />
915 <has_text text="bowtie2_se_plot" /> 932 <has_text text="bowtie2_se_plot" />
916 <has_text text="hisat2_se_plot" /> 933 <has_text text="hisat2_se_plot" />
917 <has_text text="kallisto_alignment" /> 934 <has_text text="kallisto_alignment" />
935 <has_text text="MACS2" />
918 <has_text text="star_alignment_plot" /> 936 <has_text text="star_alignment_plot" />
919 <has_text text="tophat_alignment" /> 937 <has_text text="tophat_alignment" />
920 <has_text text="hicexplorer" /> 938 <has_text text="hicexplorer" />
921 <has_text text="hicexplorer1_log_1" /> 939 <has_text text="hicexplorer1_log_1" />
922 </assert_contents> 940 </assert_contents>
926 <element name="bowtie2" file="bowtie2_stats.tabular" compare="sim_size" delta="20"/> 944 <element name="bowtie2" file="bowtie2_stats.tabular" compare="sim_size" delta="20"/>
927 <element name="general_stats" file="aligner_soft_stats.tabular" compare="sim_size" delta="50"/> 945 <element name="general_stats" file="aligner_soft_stats.tabular" compare="sim_size" delta="50"/>
928 <element name="hisat2" file="hisat2_stats.tabular" compare="sim_size" delta="20"/> 946 <element name="hisat2" file="hisat2_stats.tabular" compare="sim_size" delta="20"/>
929 <!-- <element name="hicexplorer" file="hicexplorer_stats.tabular" compare="sim_size" delta="0"/> --> 947 <!-- <element name="hicexplorer" file="hicexplorer_stats.tabular" compare="sim_size" delta="0"/> -->
930 <element name="kallisto" file="kallisto_stats.tabular" compare="sim_size" delta="10"/> 948 <element name="kallisto" file="kallisto_stats.tabular" compare="sim_size" delta="10"/>
949 <element name="macs" file="macs_stats.tabular" compare="sim_size" delta="10"/>
931 <element name="star" file="star_stats.tabular" compare="sim_size" delta="10"/> 950 <element name="star" file="star_stats.tabular" compare="sim_size" delta="10"/>
932 <element name="tophat.txt" file="tophat_stats.tabular" compare="sim_size" delta="10"/> 951 <element name="tophat.txt" file="tophat_stats.tabular" compare="sim_size" delta="10"/>
933 </output_collection> 952 </output_collection>
934 </test> 953 </test>
935 <test> 954 <test>