Mercurial > repos > iuc > multiqc

annotate multiqc.xml @ 29:ef6bd40a30d2 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4095773348da6faeb6096f58785b66898b09befa
author iuc
date Fri, 10 Oct 2025 20:11:35 +0000
parents e99aaf069191
children
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85613e9ad431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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parents: 21
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1 <tool id="multiqc" name="MultiQC" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
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2 <description>aggregate results from bioinformatics analyses into a single report</description>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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3 <macros>
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4 <import>macros.xml</import>
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5 <import>bamtools_plugin.xml</import>
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6 <import>bcftools_plugin.xml</import>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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7 <import>bismark_plugin.xml</import>
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8 <import>bowtie2_plugin.xml</import>
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9 <import>busco_plugin.xml</import>
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10 <import>cutadapt_plugin.xml</import>
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parents: 23
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11 <import>deeptools_plugin.xml</import>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
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12 <import>fastqc_plugin.xml</import>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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13 <import>fastp_plugin.xml</import>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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14 <import>featurecounts_plugin.xml</import>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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15 <import>flexbar_plugin.xml</import>
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16 <import>gatk_plugin.xml</import>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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17 <import>picard_plugin.xml</import>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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18 <import>pycoqc_plugin.xml</import>
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19 <import>qualimap_plugin.xml</import>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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20 <import>rseqc_plugin.xml</import>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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21 <import>salmon_plugin.xml</import>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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22 <import>samtools_plugin.xml</import>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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23 <import>star_plugin.xml</import>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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24 <import>trimmomatic_plugin.xml</import>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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25 <import>vcftools_plugin.xml</import>
27
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26 <import>kraken_plugin.xml</import>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
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27 <import>diamond_plugin.xml</import>
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28 <import>bakta_plugin.xml</import>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
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29 <import>freyja_plugin.xml</import>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
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30 <import>checkm_plugin.xml</import>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
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31 <import>pairtools_plugin.xml</import>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
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32 <import>porechop_plugin.xml</import>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
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33 <import>snippy_plugin.xml</import>
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34 <import>metaphlan_plugin.xml</import>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
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35 <import>bbduk_plugin.xml</import>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
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36 <import>megahit_plugin.xml</import>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
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37 <import>nonpareil_plugin.xml</import>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
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38 <import>gtdbtk_plugin.xml</import>
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39 <import>sambamba_plugin.xml</import>
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40 <import>image_content_plugin.xml</import>
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41 </macros>
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42 <expand macro="bio_tools"/>
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43 <expand macro="requirements"/>
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44 <version_command>multiqc --version</version_command>
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45 <command detect_errors="aggressive">
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46 <![CDATA[
8
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47 #import re
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48 #import os
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49
0
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50 die() { echo "$@" 1>&2 ; exit 1; } &&
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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51
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52 mkdir multiqc_WDir &&
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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53
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54 #set $configfile="F"
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55
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56 #for $i, $repeat in enumerate( $results )
8
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57 #set software_dir = os.path.join('multiqc_WDir', str($repeat.software_cond.software) + '_' + str($i))
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58 mkdir $software_dir &&
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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59 #if str($repeat.software_cond.software) == "bamtools"
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60 @BAMTOOLS_COMMAND@
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61 #elif str($repeat.software_cond.software) == "bcftools"
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62 @BCFTOOLS_COMMAND@
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63 #elif str($repeat.software_cond.software) == "bismark"
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64 @BISMARK_COMMAND@
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65 #elif str($repeat.software_cond.software) == "bowtie2"
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66 @BOWTIE2_COMMAND@
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67 #elif str($repeat.software_cond.software) == "busco"
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68 @BUSCO_COMMAND@
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69 #elif str($repeat.software_cond.software) == "cutadapt"
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70 @CUTADAPT_COMMAND@
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71 #elif str($repeat.software_cond.software) == "deeptools"
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72 @DEEPTOOLS_COMMAND@
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73 #elif str($repeat.software_cond.software) == "fastp"
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74 @FASTP_COMMAND@
0
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75 #elif str($repeat.software_cond.software) == "fastqc"
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76 @FASTQC_COMMAND@
0
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77 #elif str($repeat.software_cond.software) == "featureCounts"
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78 @FEATURECOUNTS_COMMAND@
0
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79 #elif str($repeat.software_cond.software) == "flexbar"
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80 @FLEXBAR_COMMAND@
0
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81 #elif str($repeat.software_cond.software) == "gatk"
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82 @GATK_COMMAND@
0
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83 #elif str($repeat.software_cond.software) == "hicup"
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84 #for $file in $repeat.software_cond.input
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85 @ESCAPE_IDENTIFIER@
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86 #set file_path = os.path.join($software_dir, 'HiCUP_summary_report_' + str($identifier))
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87 ln -s '${file}' '$file_path' &&
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diff changeset
88 #end for
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
89 #elif str($repeat.software_cond.software) == "hisat2"
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
90 #set $pattern = "HISAT2 summary stats:"
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
91 @LN_FILES@
6
8cb0a6c3166c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361
iuc
parents: 5
diff changeset
92 #elif str($repeat.software_cond.software) == "hicexplorer"
8cb0a6c3166c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361
iuc
parents: 5
diff changeset
93 #set $pattern = "Min rest. site distance"
8cb0a6c3166c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361
iuc
parents: 5
diff changeset
94 @LN_FILES@
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
95 #elif str($repeat.software_cond.software) == "htseq"
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
96 #set $pattern = "__too_low_aQual"
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
97 @LN_FILES@
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
98 #elif str($repeat.software_cond.software) == "kallisto"
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
99 #set $pattern = "finding pseudoalignments for the reads"
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
100 @LN_FILES@
11
46d7ad9aa59f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents: 10
diff changeset
101 #elif str($repeat.software_cond.software) == "macs2"
46d7ad9aa59f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents: 10
diff changeset
102 #set $pattern = "# This file is generated by MACS"
46d7ad9aa59f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents: 10
diff changeset
103 #for $file in $repeat.software_cond.input
46d7ad9aa59f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents: 10
diff changeset
104 @ESCAPE_IDENTIFIER@
46d7ad9aa59f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents: 10
diff changeset
105 #set file_path = os.path.join($software_dir, str($identifier) + '_peaks.xls')
46d7ad9aa59f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents: 10
diff changeset
106 grep -q "$pattern" $file || die "'$pattern' not found in the file" &&
46d7ad9aa59f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents: 10
diff changeset
107 ln -s '$file' '$file_path' &&
46d7ad9aa59f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents: 10
diff changeset
108 #end for
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
109 #elif str($repeat.software_cond.software) == "picard"
24
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
110 @PICARD_COMMAND@
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
111 #elif str($repeat.software_cond.software) == "prokka"
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
112 #set $pattern = "contigs:"
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
113 @LN_FILES@
20
9e0d04f86d87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
iuc
parents: 19
diff changeset
114 #elif str($repeat.software_cond.software) == "pycoqc"
24
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
115 @PYCOQC_COMMAND@
16
9c1131228d96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4eb6628314458d9426ea9e6fbf6e225d93e3d0fc"
iuc
parents: 15
diff changeset
116 #elif str($repeat.software_cond.software) == "qualimap"
24
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
117 @QUALIMAP_COMMAND@
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
118 #elif str($repeat.software_cond.software) == "quast"
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
119 #for $k, $file in enumerate($repeat.software_cond.input)
8
6ef9e2d46af4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 7
diff changeset
120 #set file_dir = os.path.join($software_dir, 'file_' + str($k))
6ef9e2d46af4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 7
diff changeset
121 #set file_path = os.path.join($file_dir, 'report.tsv')
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
122 mkdir '$file_dir' &&
8
6ef9e2d46af4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 7
diff changeset
123 ln -s '$file' '$file_path' &&
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
124 #end for
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
125 #elif str($repeat.software_cond.software) == "rsem"
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
126 #for $file in $repeat.software_cond.input
8
6ef9e2d46af4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 7
diff changeset
127 @ESCAPE_IDENTIFIER@
6ef9e2d46af4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 7
diff changeset
128 #set file_path = os.path.join($software_dir, str($identifier) + '.cnt')
6ef9e2d46af4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 7
diff changeset
129 ln -s '$file' '$file_path' &&
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
130 #end for
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
131 #elif str($repeat.software_cond.software) == "rseqc"
24
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
132 @RSEQC_COMMAND@
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
133 #elif str($repeat.software_cond.software) == "salmon"
24
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
134 @SALMON_COMMAND@
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
135 #elif str($repeat.software_cond.software) == "samblaster"
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
136 #set $pattern = "samblaster: Version"
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
137 @LN_FILES@
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
138 #elif str($repeat.software_cond.software) == "samtools"
24
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
139 @SAMTOOLS_COMMAND@
13
e89e08ca4d30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b
iuc
parents: 12
diff changeset
140 #elif str($repeat.software_cond.software) == "slamdunk"
e89e08ca4d30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b
iuc
parents: 12
diff changeset
141 #set $pattern = "# slamdunk"
e89e08ca4d30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b
iuc
parents: 12
diff changeset
142 @LN_FILES@
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
143 #elif str($repeat.software_cond.software) == "snpeff"
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
144 #set $pattern = "SnpEff_version"
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
145 @LN_FILES@
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
146 #elif str($repeat.software_cond.software) == "sortmerna"
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
147 #set $pattern = "Minimal SW score based on E-value"
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
148 @LN_FILES@
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
149 #else if str($repeat.software_cond.software) == "star":
24
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
150 @STAR_COMMAND@
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
151 #elif str($repeat.software_cond.software) == "tophat"
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
152 #for $file in $repeat.software_cond.input
8
6ef9e2d46af4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 7
diff changeset
153 @ESCAPE_IDENTIFIER@
6ef9e2d46af4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 7
diff changeset
154 #set file_path = os.path.join($software_dir, str($identifier) + 'align_summary.txt')
6ef9e2d46af4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 7
diff changeset
155 ln -s '$file' '$file_path' &&
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
156 #end for
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
157 #elif str($repeat.software_cond.software) == "trimmomatic"
24
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
158 @TRIMMOMATIC_COMMAND@
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
159 #elif str($repeat.software_cond.software) == "vcftools"
24
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
160 @VCFTOOLS_COMMAND@
27
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
161 #elif str($repeat.software_cond.software) == "kraken"
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
162 @KRAKEN_COMMAND@
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
163 #elif str($repeat.software_cond.software) == "diamond"
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
164 @DIAMOND_COMMAND@
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
165 #elif str($repeat.software_cond.software) == "bakta"
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
166 @BAKTA_COMMAND@
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
167 #elif str($repeat.software_cond.software) == "freyja"
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
168 @FREYJA_COMMAND@
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
169 #elif str($repeat.software_cond.software) == "checkm"
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
170 @CHECKM_COMMAND@
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
171 #elif str($repeat.software_cond.software) == "pairtools"
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
172 @PAIRTOOLS_COMMAND@
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
173 #elif str($repeat.software_cond.software) == "porechop"
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
174 @PORECHOP_COMMAND@
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
175 #elif str($repeat.software_cond.software) == "snippy"
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
176 @SNIPPY_COMMAND@
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
177 #elif str($repeat.software_cond.software) == "metaphlan"
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178 @METAPHLAN_COMMAND@
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179 #elif str($repeat.software_cond.software) == "bbduk"
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180 @BBDUK_COMMAND@
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181 #elif str($repeat.software_cond.software) == "megahit"
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182 @MEGAHIT_COMMAND@
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diff changeset
183 #elif str($repeat.software_cond.software) == "nonpareil"
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184 @NONPAREIL_COMMAND@
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185 #elif str($repeat.software_cond.software) == "gtdbtk"
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186 @GTDBTK_COMMAND@
26
1206c725e45a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
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187 #elif str($repeat.software_cond.software) == "sambamba"
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188 @SAMBAMBA_COMMAND@
0
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189 #else if str($repeat.software_cond.software) == "custom_content":
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190 #set $configfile = "T"
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191 #for $j, $file in enumerate( $repeat.software_cond.input )
8
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192 #set file_path = os.path.join($software_dir, 'file_' + str($i) + '_' + str($j))
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193 ln -s '$file' '$file_path' &&
0
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194 more $file &&
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195 #end for
1
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iuc
parents: 0
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196 #end if
0
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197 #end for
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198
28
e99aaf069191 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 7f250f4b9484eceef360ba62ef519c94b56c0b97
iuc
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199 #if str($image_content_input) != "None"
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200 @IMAGE_CONTENT_COMMAND@
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iuc
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201 #end if
e99aaf069191 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 7f250f4b9484eceef360ba62ef519c94b56c0b97
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202
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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203 multiqc multiqc_WDir
22
85613e9ad431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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204 --filename 'report'
8
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205
6ef9e2d46af4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
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206 #if str($title)
22
85613e9ad431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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207 --title '$title'
8
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208 #end if
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209 #if str($comment)
22
85613e9ad431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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210 --comment '$comment'
8
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diff changeset
211 #end if
0
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212
15
2091f142f7a2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6"
iuc
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213 $flat
18
9036f81bf82a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 2b946616b7d12eed507d95ebbd8fd257ae37d83b"
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214 $export
29
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215
0
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216 #if $configfile == "T"
8
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217 --config '$multiqc_config'
0
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218 #end if
24
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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219
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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220 &&
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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221 mkdir -p ./plots &&
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iuc
parents: 23
diff changeset
222 ls -l ./report_data/ &&
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iuc
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diff changeset
223 ##cat ./report_data/multiqc_busco.txt &&
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
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224 cp ./report_data/*plot*.txt ./plots/ | true ## don't fail if no plot files are generated
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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diff changeset
225
29
ef6bd40a30d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4095773348da6faeb6096f58785b66898b09befa
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226 #if $png_plots == "true"
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227 && mkdir -p ./png_plots
ef6bd40a30d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4095773348da6faeb6096f58785b66898b09befa
iuc
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228 && cp ./report_plots/png/*.png ./png_plots/ | true ## don't fail if no png plots are generated
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229 #end if
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iuc
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diff changeset
230
0
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iuc
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231 ]]></command>
24
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iuc
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diff changeset
232 <expand macro="configfile"/>
0
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iuc
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233 <inputs>
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234 <repeat name="results" title="Results" min="1">
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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235 <conditional name="software_cond">
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iuc
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236 <param name="software" type="select" label="Which tool was used generate logs?" help="Software name">
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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237 <!--<option value="adapterRemoval">Adapter Removal</option>-->
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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238 <!--<option value="afterqc">AfterQC</option>-->
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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239 <option value="bamtools">Bamtools</option>
8
6ef9e2d46af4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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240 <!--<option value="bbmap">BBMap</option>-->
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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241 <option value="bcftools">Bcftools</option>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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242 <!--<option value="bcl2fastq">bcl2fastq</option>-->
16
9c1131228d96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4eb6628314458d9426ea9e6fbf6e225d93e3d0fc"
iuc
parents: 15
diff changeset
243 <!--<option value="biobambam2">biobambam2</option>-->
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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244 <!--<option value="biobloomtools">BioBloom Tools</option>-->
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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245 <option value="bismark">Bismark</option>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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246 <!--<option value="bowtie1">Bowtie 1</option>-->
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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247 <option value="bowtie2">Bowtie 2</option>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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248 <option value="busco">BUSCO</option>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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249 <!--<option value="clusterflow">Cluster Flow</option>-->
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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250 <option value="cutadapt">Cutadapt/Trim Galore!</option>
8
6ef9e2d46af4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 7
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251 <!--<option value="clipandmerge">ClipAndMerge</option>-->
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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252 <!--<option value="conpair">Conpair</option>-->
8
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iuc
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253 <!--<option value="dedup">DeDup</option>-->
6ef9e2d46af4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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diff changeset
254 <option value="deeptools">deepTools</option>
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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255 <!--<option value="disambiguate">Disambiguate</option>-->
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iuc
parents:
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256 <!--<option value="fastq_screen">FastQ Screen</option>-->
12
a7e3e7e1019c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984
iuc
parents: 11
diff changeset
257 <option value="fastp">fastp</option>
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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258 <option value="fastqc">FastQC</option>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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259 <option value="featureCounts">featureCounts</option>
16
9c1131228d96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4eb6628314458d9426ea9e6fbf6e225d93e3d0fc"
iuc
parents: 15
diff changeset
260 <!--<option value="fgbio">fgbio</option>-->
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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261 <option value="flexbar">Flexbar</option>
8
6ef9e2d46af4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 7
diff changeset
262 <option value="gatk">GATK</option>
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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263 <!--<option value="goleft_indexcov">goleft indexcov</option>-->
6
8cb0a6c3166c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361
iuc
parents: 5
diff changeset
264 <option value="hicexplorer">HiCExplorer</option>
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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265 <!--<option value="hicup">HiCUP</option>-->
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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266 <option value="hisat2">HISAT2</option>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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267 <!--<option value="homer">HOMER</option>-->
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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268 <option value="htseq">HTSeq</option>
8
6ef9e2d46af4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 7
diff changeset
269 <!--<option value="interop">InterOp</option>-->
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
270 <!--<option value="jellyfish">Jellyfish</option>-->
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
271 <option value="kallisto">Kallisto</option>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
272 <!--<option value="leehom">leeHom</option>-->
11
46d7ad9aa59f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents: 10
diff changeset
273 <option value="macs2">MACS2</option>
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
274 <!--<option value="methylQA">methylQA</option>-->
16
9c1131228d96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4eb6628314458d9426ea9e6fbf6e225d93e3d0fc"
iuc
parents: 15
diff changeset
275 <!--<option value="mosdepth">mostdepth</option>-->
9c1131228d96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4eb6628314458d9426ea9e6fbf6e225d93e3d0fc"
iuc
parents: 15
diff changeset
276 <!--<option value="mtnucratio">mtnucratio</option>-->
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
277 <!--<option value="peddy">Peddy</option>-->
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
278 <option value="picard">Picard</option>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
279 <!--<option value="preseq">Preseq</option>-->
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
280 <option value="prokka">Prokka</option>
20
9e0d04f86d87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
iuc
parents: 19
diff changeset
281 <option value="pycoqc">PycoQC</option>
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
282 <!--<option value="qorts">QoRTs</option>-->
16
9c1131228d96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4eb6628314458d9426ea9e6fbf6e225d93e3d0fc"
iuc
parents: 15
diff changeset
283 <option value="qualimap">Qualimap (BamQC or RNASeq output)</option>
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
284 <option value="quast">QUAST</option>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
285 <!--<option value="rna_seqc">RNA-SeQC</option>-->
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
286 <!--<option value="rsem">RSEM (rsem-calculate-regex output)</option>-->
8
6ef9e2d46af4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 7
diff changeset
287 <option value="rseqc">RSeQC</option>
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
288 <!--<option value="salmon">Salmon</option>-->
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
289 <option value="samblaster">Samblaster</option>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
290 <option value="samtools">Samtools</option>
26
1206c725e45a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
iuc
parents: 24
diff changeset
291 <option value="sambamba">Sambamba</option>
8
6ef9e2d46af4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 7
diff changeset
292 <!--<option value="sargasso">Sargasso</option>-->
16
9c1131228d96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4eb6628314458d9426ea9e6fbf6e225d93e3d0fc"
iuc
parents: 15
diff changeset
293 <!--<option value="seqyclean">SeqyClean</option>-->
9c1131228d96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4eb6628314458d9426ea9e6fbf6e225d93e3d0fc"
iuc
parents: 15
diff changeset
294 <!--<option value="sexdeterrmine">SexDetErrmine</option>-->
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
295 <!--<option value="skewer">Skewer</option>-->
13
e89e08ca4d30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b
iuc
parents: 12
diff changeset
296 <option value="slamdunk">Slamdunk</option>
8
6ef9e2d46af4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 7
diff changeset
297 <option value="snpeff">SnpEff</option>
6ef9e2d46af4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 7
diff changeset
298 <option value="sortmerna">SortMeRNA</option>
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
299 <option value="star">STAR</option>
8
6ef9e2d46af4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 7
diff changeset
300 <!--<option value="supernova">Supernova</option>-->
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
301 <!--<option value="theta2">THeTA2</option>-->
24
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
302 <option value="tophat">TopHat2 (TopHat2 is deprecated you should not use it)</option>
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
303 <option value="trimmomatic">Trimmomatic</option>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
304 <option value="vcftools">VCFTools</option>
27
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
305 <option value="kraken">Kraken 1 or 2</option>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
306 <option value="diamond">DIAMOND</option>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
307 <option value="bakta">Bakta</option>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
308 <option value="freyja">Freyja</option>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
309 <option value="checkm">CheckM</option>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
310 <option value="pairtools">pairtools</option>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
311 <option value="porechop">Porechop</option>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
312 <option value="snippy">Snippy</option>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
313 <option value="metaphlan">MetaPhlAn</option>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
314 <option value="bbduk">BBDuk</option>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
315 <option value="megahit">MEGAHIT</option>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
316 <option value="nonpareil">Nonpareil</option>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
317 <option value="gtdbtk">GTDB-Tk</option>
8
6ef9e2d46af4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 7
diff changeset
318 <!--<option value="verifybamid">VerifyBAMID</option>-->
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
319 <!--Custom-->
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
320 <option value="custom_content">Custom Content</option>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
321 </param>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
322 <when value="bamtools">
24
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
323 <expand macro="bamtools_form"/>
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
324 </when>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
325 <when value="bcftools">
24
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
326 <expand macro="bcftools_form"/>
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
327 </when>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
328 <when value="bismark">
24
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
329 <expand macro="bismark_form"/>
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
330 </when>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
331 <when value="bowtie2">
24
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
332 <expand macro="bowtie2_form"/>
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
333 </when>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
334 <when value="busco">
24
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
335 <expand macro="busco_form"/>
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
336 </when>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
337 <when value="cutadapt">
24
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
338 <expand macro="cutadapt_form"/>
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
339 </when>
8
6ef9e2d46af4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 7
diff changeset
340 <when value="deeptools">
24
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
341 <expand macro="deeptools_form"/>
8
6ef9e2d46af4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 7
diff changeset
342 </when>
12
a7e3e7e1019c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984
iuc
parents: 11
diff changeset
343 <when value="fastp">
24
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
344 <expand macro="fastp_form"/>
12
a7e3e7e1019c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984
iuc
parents: 11
diff changeset
345 </when>
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
346 <when value="fastqc">
24
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
347 <expand macro="fastqc_form"/>
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
348 </when>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
349 <when value="featureCounts">
24
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
350 <expand macro="featurecounts_form"/>
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
351 </when>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
352 <when value="flexbar">
24
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
353 <expand macro="flexbar_form"/>
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
354 </when>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
355 <when value="gatk">
24
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
356 <expand macro="gatk_form"/>
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
357 </when>
6
8cb0a6c3166c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361
iuc
parents: 5
diff changeset
358 <when value="hicexplorer">
8cb0a6c3166c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361
iuc
parents: 5
diff changeset
359 <param name="input" type="data" format="txt,tabular" multiple="true" label="Output of HiCExplorer" help="It should contain 'Min rest. site distance'"/>
8cb0a6c3166c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361
iuc
parents: 5
diff changeset
360 </when>
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
361 <when value="hisat2">
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
362 <param name="input" type="data" format="txt,tabular" multiple="true" label="Output of HISAT2" help="It should contain 'HISAT2 summary stats:'"/>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
363 </when>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
364 <when value="htseq">
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
365 <param name="input" type="data" format="txt,tabular" multiple="true" label="Output of HTSeq" help="It should contain '__too_low_aQual'"/>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
366 </when>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
367 <when value="kallisto">
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
368 <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'"/>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
369 </when>
11
46d7ad9aa59f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents: 10
diff changeset
370 <when value="macs2">
46d7ad9aa59f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents: 10
diff changeset
371 <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'"/>
46d7ad9aa59f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents: 10
diff changeset
372 </when>
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
373 <when value="picard">
24
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
374 <expand macro="picard_form"/>
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
375 </when>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
376 <when value="prokka">
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
377 <param name="input" type="data" format="txt" multiple="true" label="Output of Prokka" help="It should contain 'contigs:'"/>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
378 </when>
20
9e0d04f86d87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
iuc
parents: 19
diff changeset
379 <when value="pycoqc">
24
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
380 <expand macro="pycoqc_form"/>
20
9e0d04f86d87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
iuc
parents: 19
diff changeset
381 </when>
16
9c1131228d96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4eb6628314458d9426ea9e6fbf6e225d93e3d0fc"
iuc
parents: 15
diff changeset
382 <when value="qualimap">
24
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
383 <expand macro="qualimap_form"/>
16
9c1131228d96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4eb6628314458d9426ea9e6fbf6e225d93e3d0fc"
iuc
parents: 15
diff changeset
384 </when>
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
385 <when value="quast">
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
386 <param name="input" type="data" format="tabular,tsv" multiple="true" label="Output of Quast"/>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
387 </when>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
388 <when value="rseqc">
24
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
389 <expand macro="rseqc_form"/>
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
390 </when>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
391 <when value="samblaster">
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
392 <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of Samblaster" help="It should contain 'samblaster: Version'"/>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
393 </when>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
394 <when value="samtools">
24
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
395 <expand macro="samtools_form"/>
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
396 </when>
13
e89e08ca4d30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b
iuc
parents: 12
diff changeset
397 <when value="slamdunk">
e89e08ca4d30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b
iuc
parents: 12
diff changeset
398 <param name="input" type="data" format="txt,tabular" multiple="true" label="Output of Slamdunk Alleyoop" help="It should contain '# slamdunk'"/>
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
399 </when>
8
6ef9e2d46af4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 7
diff changeset
400 <when value="snpeff">
6ef9e2d46af4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 7
diff changeset
401 <param name="input" type="data" format="csv" multiple="true" label="Output of SnpEff"/>
6ef9e2d46af4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 7
diff changeset
402 </when>
13
e89e08ca4d30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b
iuc
parents: 12
diff changeset
403 <when value="sortmerna">
e89e08ca4d30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b
iuc
parents: 12
diff changeset
404 <param name="input" type="data" format="txt" multiple="true" label="Log file of SortMeRNA" help="It should contain 'Minimal SW score based on E-value'"/>
e89e08ca4d30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b
iuc
parents: 12
diff changeset
405 </when>
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
406 <when value="star">
24
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
407 <expand macro="star_form"/>
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
408 </when>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
409 <when value="tophat">
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
410 <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of TopHat2"/>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
411 </when>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
412 <when value="trimmomatic">
24
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
413 <expand macro="trimmomatic_form"/>
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
414 </when>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
415 <when value="vcftools">
24
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
416 <expand macro="vcftools_form"/>
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
417 </when>
27
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
418 <when value="kraken">
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
419 <expand macro="kraken_form"/>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
420 </when>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
421 <when value="diamond">
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
422 <expand macro="diamond_form"/>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
423 </when>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
424 <when value="bakta">
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
425 <expand macro="bakta_form"/>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
426 </when>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
427 <when value="freyja">
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
428 <expand macro="freyja_form"/>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
429 </when>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
430 <when value="checkm">
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
431 <expand macro="checkm_form"/>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
432 </when>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
433 <when value="pairtools">
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
434 <expand macro="pairtools_form"/>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
435 </when>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
436 <when value="porechop">
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
437 <expand macro="porechop_form"/>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
438 </when>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
439 <when value="snippy">
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
440 <expand macro="snippy_form"/>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
441 </when>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
442 <when value="metaphlan">
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
443 <expand macro="metaphlan_form"/>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
444 </when>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
445 <when value="bbduk">
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
446 <expand macro="bbduk_form"/>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
447 </when>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
448 <when value="megahit">
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
449 <expand macro="megahit_form"/>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
450 </when>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
451 <when value="nonpareil">
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
452 <expand macro="nonpareil_form"/>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
453 </when>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
454 <when value="gtdbtk">
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
455 <expand macro="gtdbtk_form"/>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
diff changeset
456 </when>
26
1206c725e45a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
iuc
parents: 24
diff changeset
457 <when value="sambamba">
1206c725e45a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
iuc
parents: 24
diff changeset
458 <expand macro="sambamba_form"/>
1206c725e45a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
iuc
parents: 24
diff changeset
459 </when>
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
460 <when value="custom_content">
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
461 <param argument="plot_type" label="The plot type to visualise the data with" type="select">
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
462 <option value="linegraph">linegraph</option>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
463 <option value="bargraph">bargraph</option>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
464 <option value="scatter">scatter</option>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
465 <option value="generalstats">generalstats</option>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
466 <option value="table">table</option>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
467 </param>
24
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
468 <param argument="section_name" label="Section name" type="text" help="Nice name used for the report section header"/>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
469 <param argument="title" label="Title" type="text" help="Plot title"/>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
470 <param argument="description" label="Description" type="text" help="Introductory text to be printed under the section header"/>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
471 <param argument="xlab" label="X axis label" type="text"/>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
472 <param argument="ylab" label="Y axis label" type="text"/>
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
473 <param name="input" type="data" format="tabular,tsv" multiple="true" label="Data files"/>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
474 </when>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
475 </conditional>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
476 </repeat>
28
e99aaf069191 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 7f250f4b9484eceef360ba62ef519c94b56c0b97
iuc
parents: 27
diff changeset
477 <expand macro="image_content_form"/>
22
85613e9ad431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents: 21
diff changeset
478 <param name="title" type="text" value="" optional="true" label="Report title" help="It is printed as page header">
85613e9ad431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents: 21
diff changeset
479 <sanitizer invalid_char="">
85613e9ad431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents: 21
diff changeset
480 <valid initial="string.letters,string.digits">
24
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
481 <add value=","/>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
482 <add value=":"/>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
483 <add value="-"/>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
484 <add value="_"/>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
485 <add value=" "/>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
486 <add value="."/>
22
85613e9ad431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents: 21
diff changeset
487 </valid>
85613e9ad431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents: 21
diff changeset
488 </sanitizer>
85613e9ad431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents: 21
diff changeset
489 <validator type="regex">[0-9a-zA-Z,: _.-]+</validator>
85613e9ad431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents: 21
diff changeset
490 </param>
85613e9ad431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents: 21
diff changeset
491 <param name="comment" type="text" value="" optional="true" label="Custom comment" help="It will be printed at the top of the report">
85613e9ad431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents: 21
diff changeset
492 <sanitizer invalid_char="">
85613e9ad431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents: 21
diff changeset
493 <valid initial="string.letters,string.digits">
24
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
494 <add value=","/>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
495 <add value=":"/>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
496 <add value="-"/>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
497 <add value="_"/>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
498 <add value=" "/>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
499 <add value="."/>
22
85613e9ad431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents: 21
diff changeset
500 </valid>
85613e9ad431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents: 21
diff changeset
501 </sanitizer>
85613e9ad431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents: 21
diff changeset
502 <validator type="regex">[0-9a-zA-Z,: _.-]+</validator>
85613e9ad431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents: 21
diff changeset
503 </param>
17
71f3455819a0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 263b1803fbf2622dbeb283b1d965690a5dc24ec9"
iuc
parents: 16
diff changeset
504 <param argument="--flat" type="boolean" truevalue="--flat" falsevalue="" checked="false" label="Use only flat plots (non-interactive images)" help="To consume less disk space and resources to display. Used by default when there are 100 or more samples."/>
18
9036f81bf82a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 2b946616b7d12eed507d95ebbd8fd257ae37d83b"
iuc
parents: 17
diff changeset
505 <param argument="--export" type="boolean" truevalue="--export" falsevalue="" checked="false" label="Output the multiQC plots raw data?" help="This will output a file for each plot containing the raw data used to generate the plot"/>
29
ef6bd40a30d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4095773348da6faeb6096f58785b66898b09befa
iuc
parents: 28
diff changeset
506 <param name="png_plots" type="boolean" truevalue="true" falsevalue="false" label="Output PNG plots?" help="Choose if you want PNG plots in an output collection"/>
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
507 </inputs>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
508 <outputs>
24
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
509 <data name="html_report" format="html" from_work_dir="report.html" label="${tool.name} on ${on_string}: Webpage"/>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
510 <data name="stats" format="tabular" from_work_dir="report_data/multiqc_general_stats.txt" label="${tool.name} on ${on_string}: Stats"/>
15
2091f142f7a2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6"
iuc
parents: 13
diff changeset
511 <collection name="plots" type="list" label="${tool.name} on ${on_string}: Plots">
24
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
512 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tabular" directory="plots"/>
18
9036f81bf82a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 2b946616b7d12eed507d95ebbd8fd257ae37d83b"
iuc
parents: 17
diff changeset
513 <filter>export</filter>
15
2091f142f7a2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6"
iuc
parents: 13
diff changeset
514 </collection>
29
ef6bd40a30d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4095773348da6faeb6096f58785b66898b09befa
iuc
parents: 28
diff changeset
515 <collection name="png_plot" type="list" label="${tool.name} on ${on_string}: PNG Plots">
ef6bd40a30d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4095773348da6faeb6096f58785b66898b09befa
iuc
parents: 28
diff changeset
516 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.png" format="png" directory="png_plots"/>
ef6bd40a30d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4095773348da6faeb6096f58785b66898b09befa
iuc
parents: 28
diff changeset
517 <filter>png_plots</filter>
ef6bd40a30d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4095773348da6faeb6096f58785b66898b09befa
iuc
parents: 28
diff changeset
518 </collection>
0
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
519 </outputs>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
520 <tests>
24
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
521 <expand macro="general_tests"/>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
522 <expand macro="bcftools_test"/>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
523 <expand macro="bowtie2_test"/>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
524 <expand macro="fastqc_test"/>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
525 <expand macro="trimmomatic_test"/>
29
ef6bd40a30d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4095773348da6faeb6096f58785b66898b09befa
iuc
parents: 28
diff changeset
526 <!-- Test 10 -->
24
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
527 <expand macro="flexbar_test"/>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
528 <expand macro="fastp_test"/>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
529 <expand macro="bismark_test"/>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
530 <expand macro="rseqc_test"/>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
531 <expand macro="star_test"/>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
532 <expand macro="cutadapt_test"/>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
533 <expand macro="samtools_test"/>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
534 <expand macro="busco_test"/>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
535 <expand macro="featurecounts_test"/>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
536 <expand macro="picard_test"/>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
537 <!-- Test 20 -->
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
538 <expand macro="qualimap_test"/>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents: 23
diff changeset
539 <expand macro="gatk_test"/>
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540 <expand macro="bamtools_test"/>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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541 <expand macro="pycoqc_test"/>
27
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diff changeset
542 <expand macro="kraken_test"/>
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543 <expand macro="diamond_test"/>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
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544 <expand macro="bakta_test"/>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
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parents: 26
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545 <expand macro="freyja_test"/>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
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parents: 26
diff changeset
546 <expand macro="checkm_test"/>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
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parents: 26
diff changeset
547 <expand macro="pairtools_test"/>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
iuc
parents: 26
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548 <expand macro="porechop_test"/>
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parents: 26
diff changeset
549 <expand macro="snippy_test"/>
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550 <expand macro="metaphlan_test"/>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
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551 <expand macro="bbduk_test"/>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
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552 <expand macro="megahit_test"/>
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parents: 26
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553 <expand macro="nonpareil_test"/>
b7e8663db1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
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parents: 26
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554 <expand macro="gtdbtk_test"/>
26
1206c725e45a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
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parents: 24
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555 <expand macro="sambamba_test"/>
24
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556 <!--expand macro="vcftools_test"/> Does not work, did it ever worked? -->
29
ef6bd40a30d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4095773348da6faeb6096f58785b66898b09befa
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parents: 28
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557
0
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558 </tests>
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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559 <help><![CDATA[
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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560 **What it does**
b437798cb165 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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561
24
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562 `MultiQC <http://multiqc.info/>`_ aggregates results from bioinformatics analyses across many samples into a single report.
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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563 It takes results of multiple analyses and creates a report that can be viewed as a single beautiful web-page.
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564 It's a general use tool, perfect for summarizing the output from numerous bioinformatics tools.
0
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565
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566 **Inputs**
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567
24
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568 MultiQC takes software output summaries/logs and creates a single report from them. You need to tell the tool which software was used to generate the report.
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569 This is done using the **Software name** dropdown. At present only the Galaxy tools found in the ToolShed produce logs that can used with MultiQC
0
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570
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571 ]]></help>
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572 <citations>
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573 <citation type="doi">10.1093/bioinformatics/btw354</citation>
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574 </citations>
24
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575 <creator>
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576 <person givenName="Cyril" familyName="Monjeaud" url="https://github.com/cmonjeau"/>
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577 <person givenName="Yvan" familyName="Le Bras" url="https://github.com/yvanlebras"/>
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578 <person givenName="Bérénice" familyName="Batut" url="https://github.com/bebatut"/>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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parents: 23
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579 <person givenName="Björn" familyName="Grüning" url="https://github.com/bgruening"/>
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parents: 23
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580 </creator>
0
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581 </tool>