Mercurial > repos > iuc > multiqc
annotate multiqc.xml @ 24:0771dee34cff draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
| author | iuc |
|---|---|
| date | Mon, 02 Sep 2024 14:22:19 +0000 |
| parents | d01bcfd04189 |
| children | 1206c725e45a |
| rev | line source |
|---|---|
|
22
85613e9ad431
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
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1 <tool id="multiqc" name="MultiQC" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> |
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0
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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2 <description>aggregate results from bioinformatics analyses into a single report</description> |
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b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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3 <macros> |
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22
85613e9ad431
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
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4 <import>macros.xml</import> |
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24
0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
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5 <import>bamtools_plugin.xml</import> |
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0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
23
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6 <import>bcftools_plugin.xml</import> |
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0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
23
diff
changeset
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7 <import>bismark_plugin.xml</import> |
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0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
23
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changeset
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8 <import>bowtie2_plugin.xml</import> |
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0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
23
diff
changeset
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9 <import>busco_plugin.xml</import> |
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0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
23
diff
changeset
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10 <import>cutadapt_plugin.xml</import> |
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0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
23
diff
changeset
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11 <import>deeptools_plugin.xml</import> |
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0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
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12 <import>fastqc_plugin.xml</import> |
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0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
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diff
changeset
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13 <import>fastp_plugin.xml</import> |
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0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
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changeset
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14 <import>featurecounts_plugin.xml</import> |
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0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
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changeset
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15 <import>flexbar_plugin.xml</import> |
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0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
23
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changeset
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16 <import>gatk_plugin.xml</import> |
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0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
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changeset
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17 <import>picard_plugin.xml</import> |
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0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
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changeset
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18 <import>pycoqc_plugin.xml</import> |
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0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
23
diff
changeset
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19 <import>qualimap_plugin.xml</import> |
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0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
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changeset
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20 <import>rseqc_plugin.xml</import> |
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0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
23
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changeset
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21 <import>salmon_plugin.xml</import> |
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0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
23
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changeset
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22 <import>samtools_plugin.xml</import> |
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0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
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changeset
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23 <import>star_plugin.xml</import> |
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0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
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changeset
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24 <import>trimmomatic_plugin.xml</import> |
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0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
23
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changeset
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25 <import>vcftools_plugin.xml</import> |
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0
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
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26 </macros> |
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22
85613e9ad431
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
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27 <expand macro="bio_tools"/> |
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24
0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
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28 <expand macro="requirements"/> |
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08188e2202aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit cb4a49f04475c7f6e2d304ded739c63db9f29724
iuc
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29 <version_command>multiqc --version</version_command> |
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0
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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30 <command detect_errors="aggressive"> |
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b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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31 <![CDATA[ |
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6ef9e2d46af4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
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32 #import re |
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6ef9e2d46af4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
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33 #import os |
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6ef9e2d46af4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
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34 |
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0
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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35 die() { echo "$@" 1>&2 ; exit 1; } && |
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b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
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36 |
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b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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37 mkdir multiqc_WDir && |
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b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
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38 |
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b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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39 #set $configfile="F" |
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b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
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40 |
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b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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41 #for $i, $repeat in enumerate( $results ) |
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8
6ef9e2d46af4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
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42 #set software_dir = os.path.join('multiqc_WDir', str($repeat.software_cond.software) + '_' + str($i)) |
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0
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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43 mkdir $software_dir && |
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b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
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44 #if str($repeat.software_cond.software) == "bamtools" |
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24
0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
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45 @BAMTOOLS_COMMAND@ |
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0
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
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46 #elif str($repeat.software_cond.software) == "bcftools" |
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24
0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
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47 @BCFTOOLS_COMMAND@ |
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0
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
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48 #elif str($repeat.software_cond.software) == "bismark" |
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24
0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
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49 @BISMARK_COMMAND@ |
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0
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
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50 #elif str($repeat.software_cond.software) == "bowtie2" |
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24
0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
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51 @BOWTIE2_COMMAND@ |
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b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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52 #elif str($repeat.software_cond.software) == "busco" |
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24
0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
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53 @BUSCO_COMMAND@ |
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0
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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54 #elif str($repeat.software_cond.software) == "cutadapt" |
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24
0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
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55 @CUTADAPT_COMMAND@ |
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6ef9e2d46af4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
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56 #elif str($repeat.software_cond.software) == "deeptools" |
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24
0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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57 @DEEPTOOLS_COMMAND@ |
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a7e3e7e1019c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984
iuc
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58 #elif str($repeat.software_cond.software) == "fastp" |
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24
0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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59 @FASTP_COMMAND@ |
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0
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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60 #elif str($repeat.software_cond.software) == "fastqc" |
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24
0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
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61 @FASTQC_COMMAND@ |
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0
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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62 #elif str($repeat.software_cond.software) == "featureCounts" |
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24
0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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63 @FEATURECOUNTS_COMMAND@ |
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0
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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64 #elif str($repeat.software_cond.software) == "flexbar" |
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24
0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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65 @FLEXBAR_COMMAND@ |
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0
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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66 #elif str($repeat.software_cond.software) == "gatk" |
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24
0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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67 @GATK_COMMAND@ |
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0
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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68 #elif str($repeat.software_cond.software) == "hicup" |
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b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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69 #for $file in $repeat.software_cond.input |
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6ef9e2d46af4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
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70 @ESCAPE_IDENTIFIER@ |
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6ef9e2d46af4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
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71 #set file_path = os.path.join($software_dir, 'HiCUP_summary_report_' + str($identifier)) |
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6ef9e2d46af4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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72 ln -s '${file}' '$file_path' && |
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b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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73 #end for |
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b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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74 #elif str($repeat.software_cond.software) == "hisat2" |
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b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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75 #set $pattern = "HISAT2 summary stats:" |
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b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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76 @LN_FILES@ |
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8cb0a6c3166c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361
iuc
parents:
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77 #elif str($repeat.software_cond.software) == "hicexplorer" |
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8cb0a6c3166c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361
iuc
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78 #set $pattern = "Min rest. site distance" |
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8cb0a6c3166c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361
iuc
parents:
5
diff
changeset
|
79 @LN_FILES@ |
|
0
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
80 #elif str($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
|
81 #set $pattern = "__too_low_aQual" |
|
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
82 @LN_FILES@ |
|
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
83 #elif str($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
|
84 #set $pattern = "finding pseudoalignments for the reads" |
|
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
85 @LN_FILES@ |
|
11
46d7ad9aa59f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents:
10
diff
changeset
|
86 #elif str($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
|
87 #set $pattern = "# This file is generated by MACS" |
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46d7ad9aa59f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents:
10
diff
changeset
|
88 #for $file in $repeat.software_cond.input |
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46d7ad9aa59f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents:
10
diff
changeset
|
89 @ESCAPE_IDENTIFIER@ |
|
46d7ad9aa59f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents:
10
diff
changeset
|
90 #set file_path = os.path.join($software_dir, str($identifier) + '_peaks.xls') |
|
46d7ad9aa59f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents:
10
diff
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91 grep -q "$pattern" $file || die "'$pattern' not found in the file" && |
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46d7ad9aa59f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents:
10
diff
changeset
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92 ln -s '$file' '$file_path' && |
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46d7ad9aa59f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents:
10
diff
changeset
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93 #end for |
|
0
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
94 #elif str($repeat.software_cond.software) == "picard" |
|
24
0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
23
diff
changeset
|
95 @PICARD_COMMAND@ |
|
0
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
96 #elif str($repeat.software_cond.software) == "prokka" |
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b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
97 #set $pattern = "contigs:" |
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b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
98 @LN_FILES@ |
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20
9e0d04f86d87
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
iuc
parents:
19
diff
changeset
|
99 #elif str($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:
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diff
changeset
|
100 @PYCOQC_COMMAND@ |
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16
9c1131228d96
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4eb6628314458d9426ea9e6fbf6e225d93e3d0fc"
iuc
parents:
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diff
changeset
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101 #elif str($repeat.software_cond.software) == "qualimap" |
|
24
0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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102 @QUALIMAP_COMMAND@ |
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0
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
103 #elif str($repeat.software_cond.software) == "quast" |
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b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
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104 #for $k, $file in enumerate($repeat.software_cond.input) |
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8
6ef9e2d46af4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
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105 #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:
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diff
changeset
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106 #set file_path = os.path.join($file_dir, 'report.tsv') |
|
0
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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changeset
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107 mkdir '$file_dir' && |
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8
6ef9e2d46af4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
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diff
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108 ln -s '$file' '$file_path' && |
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0
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
109 #end for |
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b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
110 #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
|
111 #for $file in $repeat.software_cond.input |
|
8
6ef9e2d46af4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
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112 @ESCAPE_IDENTIFIER@ |
|
6ef9e2d46af4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
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113 #set file_path = os.path.join($software_dir, str($identifier) + '.cnt') |
|
6ef9e2d46af4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
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diff
changeset
|
114 ln -s '$file' '$file_path' && |
|
0
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
115 #end for |
|
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
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116 #elif str($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
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117 @RSEQC_COMMAND@ |
|
0
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
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118 #elif str($repeat.software_cond.software) == "salmon" |
|
24
0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
23
diff
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119 @SALMON_COMMAND@ |
|
0
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
120 #elif str($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
|
121 #set $pattern = "samblaster: Version" |
|
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
122 @LN_FILES@ |
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b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
123 #elif str($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
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|
124 @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
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125 #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
|
126 #set $pattern = "# slamdunk" |
|
e89e08ca4d30
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b
iuc
parents:
12
diff
changeset
|
127 @LN_FILES@ |
|
0
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
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128 #elif str($repeat.software_cond.software) == "snpeff" |
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b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
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129 #set $pattern = "SnpEff_version" |
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b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
130 @LN_FILES@ |
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b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
131 #elif str($repeat.software_cond.software) == "sortmerna" |
|
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
132 #set $pattern = "Minimal SW score based on E-value" |
|
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
133 @LN_FILES@ |
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b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
134 #else if str($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
|
135 @STAR_COMMAND@ |
|
0
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
136 #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
|
137 #for $file in $repeat.software_cond.input |
|
8
6ef9e2d46af4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
138 @ESCAPE_IDENTIFIER@ |
|
6ef9e2d46af4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
139 #set file_path = os.path.join($software_dir, str($identifier) + 'align_summary.txt') |
|
6ef9e2d46af4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
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diff
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140 ln -s '$file' '$file_path' && |
|
0
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
141 #end for |
|
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
142 #elif str($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
|
143 @TRIMMOMATIC_COMMAND@ |
|
0
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
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144 #elif str($repeat.software_cond.software) == "vcftools" |
|
24
0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
23
diff
changeset
|
145 @VCFTOOLS_COMMAND@ |
|
0
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
146 #else if str($repeat.software_cond.software) == "custom_content": |
|
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
147 #set $configfile = "T" |
|
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
148 #for $j, $file in enumerate( $repeat.software_cond.input ) |
|
8
6ef9e2d46af4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
149 #set file_path = os.path.join($software_dir, 'file_' + str($i) + '_' + str($j)) |
|
6ef9e2d46af4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
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|
150 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
|
151 more $file && |
|
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
152 #end for |
|
1
ac90f110c39c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 110247de01764a544371d07eaed0308429a47daa
iuc
parents:
0
diff
changeset
|
153 #end if |
|
0
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
154 #end for |
|
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
155 |
|
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
156 multiqc multiqc_WDir |
|
22
85613e9ad431
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
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|
157 --filename 'report' |
|
8
6ef9e2d46af4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
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diff
changeset
|
158 |
|
6ef9e2d46af4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
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159 #if str($title) |
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22
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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160 --title '$title' |
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161 #end if |
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162 #if str($comment) |
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22
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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163 --comment '$comment' |
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164 #end if |
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165 |
|
15
2091f142f7a2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6"
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166 $flat |
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18
9036f81bf82a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 2b946616b7d12eed507d95ebbd8fd257ae37d83b"
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167 $export |
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15
2091f142f7a2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6"
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168 |
|
0
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169 #if $configfile == "T" |
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170 --config '$multiqc_config' |
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171 #end if |
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24
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172 |
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173 && |
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174 mkdir -p ./plots && |
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175 ls -l ./report_data/ && |
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176 ##cat ./report_data/multiqc_busco.txt && |
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177 cp ./report_data/*plot*.txt ./plots/ | true ## don't fail if no plot files are generated |
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178 |
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179 ]]></command> |
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180 <expand macro="configfile"/> |
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181 <inputs> |
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182 <repeat name="results" title="Results" min="1"> |
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183 <conditional name="software_cond"> |
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184 <param name="software" type="select" label="Which tool was used generate logs?" help="Software name"> |
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185 <!--<option value="adapterRemoval">Adapter Removal</option>--> |
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186 <!--<option value="afterqc">AfterQC</option>--> |
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187 <option value="bamtools">Bamtools</option> |
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188 <!--<option value="bbmap">BBMap</option>--> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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189 <option value="bcftools">Bcftools</option> |
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190 <!--<option value="bcl2fastq">bcl2fastq</option>--> |
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16
9c1131228d96
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4eb6628314458d9426ea9e6fbf6e225d93e3d0fc"
iuc
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191 <!--<option value="biobambam2">biobambam2</option>--> |
|
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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192 <!--<option value="biobloomtools">BioBloom Tools</option>--> |
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193 <option value="bismark">Bismark</option> |
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194 <!--<option value="bowtie1">Bowtie 1</option>--> |
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195 <option value="bowtie2">Bowtie 2</option> |
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196 <option value="busco">BUSCO</option> |
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197 <!--<option value="clusterflow">Cluster Flow</option>--> |
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198 <option value="cutadapt">Cutadapt/Trim Galore!</option> |
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199 <!--<option value="clipandmerge">ClipAndMerge</option>--> |
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0
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200 <!--<option value="conpair">Conpair</option>--> |
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8
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iuc
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201 <!--<option value="dedup">DeDup</option>--> |
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202 <option value="deeptools">deepTools</option> |
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0
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203 <!--<option value="disambiguate">Disambiguate</option>--> |
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204 <!--<option value="fastq_screen">FastQ Screen</option>--> |
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12
a7e3e7e1019c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984
iuc
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205 <option value="fastp">fastp</option> |
|
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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206 <option value="fastqc">FastQC</option> |
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207 <option value="featureCounts">featureCounts</option> |
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16
9c1131228d96
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4eb6628314458d9426ea9e6fbf6e225d93e3d0fc"
iuc
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208 <!--<option value="fgbio">fgbio</option>--> |
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0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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209 <option value="flexbar">Flexbar</option> |
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8
6ef9e2d46af4
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210 <option value="gatk">GATK</option> |
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0
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211 <!--<option value="goleft_indexcov">goleft indexcov</option>--> |
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6
8cb0a6c3166c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361
iuc
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212 <option value="hicexplorer">HiCExplorer</option> |
|
0
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213 <!--<option value="hicup">HiCUP</option>--> |
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214 <option value="hisat2">HISAT2</option> |
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215 <!--<option value="homer">HOMER</option>--> |
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216 <option value="htseq">HTSeq</option> |
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6ef9e2d46af4
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217 <!--<option value="interop">InterOp</option>--> |
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0
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218 <!--<option value="jellyfish">Jellyfish</option>--> |
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219 <option value="kallisto">Kallisto</option> |
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220 <!--<option value="leehom">leeHom</option>--> |
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11
46d7ad9aa59f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
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221 <option value="macs2">MACS2</option> |
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0
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222 <!--<option value="methylQA">methylQA</option>--> |
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16
9c1131228d96
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4eb6628314458d9426ea9e6fbf6e225d93e3d0fc"
iuc
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223 <!--<option value="mosdepth">mostdepth</option>--> |
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9c1131228d96
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4eb6628314458d9426ea9e6fbf6e225d93e3d0fc"
iuc
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224 <!--<option value="mtnucratio">mtnucratio</option>--> |
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0
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225 <!--<option value="peddy">Peddy</option>--> |
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226 <option value="picard">Picard</option> |
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227 <!--<option value="preseq">Preseq</option>--> |
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228 <option value="prokka">Prokka</option> |
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20
9e0d04f86d87
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
iuc
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229 <option value="pycoqc">PycoQC</option> |
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0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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230 <!--<option value="qorts">QoRTs</option>--> |
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16
9c1131228d96
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4eb6628314458d9426ea9e6fbf6e225d93e3d0fc"
iuc
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231 <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
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232 <option value="quast">QUAST</option> |
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233 <!--<option value="rna_seqc">RNA-SeQC</option>--> |
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234 <!--<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
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235 <option value="rseqc">RSeQC</option> |
|
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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236 <!--<option value="salmon">Salmon</option>--> |
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237 <option value="samblaster">Samblaster</option> |
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238 <option value="samtools">Samtools</option> |
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8
6ef9e2d46af4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
239 <!--<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
|
240 <!--<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
|
241 <!--<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
|
242 <!--<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
|
243 <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
|
244 <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
|
245 <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
|
246 <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
|
247 <!--<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
|
248 <!--<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
|
249 <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
|
250 <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
|
251 <option value="vcftools">VCFTools</option> |
|
8
6ef9e2d46af4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
252 <!--<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
|
253 <!--Custom--> |
|
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
254 <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
|
255 </param> |
|
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
256 <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
|
257 <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
|
258 </when> |
|
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
259 <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
|
260 <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
|
261 </when> |
|
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
262 <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
|
263 <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
|
264 </when> |
|
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
265 <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
|
266 <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
|
267 </when> |
|
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
268 <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
|
269 <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
|
270 </when> |
|
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
271 <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
|
272 <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
|
273 </when> |
|
8
6ef9e2d46af4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
274 <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
|
275 <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
|
276 </when> |
|
12
a7e3e7e1019c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984
iuc
parents:
11
diff
changeset
|
277 <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
|
278 <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
|
279 </when> |
|
0
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
280 <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
|
281 <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
|
282 </when> |
|
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
283 <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
|
284 <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
|
285 </when> |
|
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
286 <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
|
287 <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
|
288 </when> |
|
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
289 <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
|
290 <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
|
291 </when> |
|
6
8cb0a6c3166c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361
iuc
parents:
5
diff
changeset
|
292 <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
|
293 <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
|
294 </when> |
|
0
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
295 <when value="hisat2"> |
|
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
296 <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
|
297 </when> |
|
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
298 <when value="htseq"> |
|
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
299 <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
|
300 </when> |
|
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
301 <when value="kallisto"> |
|
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
302 <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
|
303 </when> |
|
11
46d7ad9aa59f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents:
10
diff
changeset
|
304 <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
|
305 <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
|
306 </when> |
|
0
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
307 <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
|
308 <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
|
309 </when> |
|
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
310 <when value="prokka"> |
|
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
311 <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
|
312 </when> |
|
20
9e0d04f86d87
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
iuc
parents:
19
diff
changeset
|
313 <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
|
314 <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
|
315 </when> |
|
16
9c1131228d96
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4eb6628314458d9426ea9e6fbf6e225d93e3d0fc"
iuc
parents:
15
diff
changeset
|
316 <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
|
317 <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
|
318 </when> |
|
0
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
319 <when value="quast"> |
|
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
320 <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
|
321 </when> |
|
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
322 <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
|
323 <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
|
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="samblaster"> |
|
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
326 <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
|
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="samtools"> |
|
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="samtools_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> |
|
13
e89e08ca4d30
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b
iuc
parents:
12
diff
changeset
|
331 <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
|
332 <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
|
333 </when> |
|
8
6ef9e2d46af4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
334 <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
|
335 <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
|
336 </when> |
|
13
e89e08ca4d30
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b
iuc
parents:
12
diff
changeset
|
337 <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
|
338 <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
|
339 </when> |
|
0
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
340 <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
|
341 <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
|
342 </when> |
|
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
343 <when value="tophat"> |
|
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
344 <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
|
345 </when> |
|
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
346 <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
|
347 <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
|
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="vcftools"> |
|
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="vcftools_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="custom_content"> |
|
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
353 <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
|
354 <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
|
355 <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
|
356 <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
|
357 <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
|
358 <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
|
359 </param> |
|
24
0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
23
diff
changeset
|
360 <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
|
361 <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
|
362 <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
|
363 <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
|
364 <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
|
365 <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
|
366 </when> |
|
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
367 </conditional> |
|
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
368 </repeat> |
|
22
85613e9ad431
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
369 <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
|
370 <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
|
371 <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
|
372 <add value=","/> |
|
0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
23
diff
changeset
|
373 <add value=":"/> |
|
0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
23
diff
changeset
|
374 <add value="-"/> |
|
0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
23
diff
changeset
|
375 <add value="_"/> |
|
0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
23
diff
changeset
|
376 <add value=" "/> |
|
0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
23
diff
changeset
|
377 <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
|
378 </valid> |
|
85613e9ad431
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
379 </sanitizer> |
|
85613e9ad431
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
380 <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
|
381 </param> |
|
85613e9ad431
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
382 <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
|
383 <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
|
384 <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
|
385 <add value=","/> |
|
0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
23
diff
changeset
|
386 <add value=":"/> |
|
0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
23
diff
changeset
|
387 <add value="-"/> |
|
0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
23
diff
changeset
|
388 <add value="_"/> |
|
0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
23
diff
changeset
|
389 <add value=" "/> |
|
0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
23
diff
changeset
|
390 <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
|
391 </valid> |
|
85613e9ad431
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
392 </sanitizer> |
|
85613e9ad431
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
393 <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
|
394 </param> |
|
17
71f3455819a0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 263b1803fbf2622dbeb283b1d965690a5dc24ec9"
iuc
parents:
16
diff
changeset
|
395 <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
|
396 <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"/> |
|
0
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
397 </inputs> |
|
b437798cb165
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
398 <outputs> |
|
24
0771dee34cff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
23
diff
changeset
|
399 <data name="html_report" format="html" from_work_dir="report.html" label="${tool.name} on ${on_string}: Webpage"/> |
|
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400 <data name="stats" format="tabular" from_work_dir="report_data/multiqc_general_stats.txt" label="${tool.name} on ${on_string}: Stats"/> |
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401 <collection name="plots" type="list" label="${tool.name} on ${on_string}: Plots"> |
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402 <discover_datasets pattern="(?P<designation>.+)\.txt" format="tabular" directory="plots"/> |
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403 <filter>export</filter> |
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404 </collection> |
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405 </outputs> |
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406 <tests> |
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407 <expand macro="general_tests"/> |
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408 <expand macro="bcftools_test"/> |
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409 <expand macro="bowtie2_test"/> |
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410 <expand macro="fastqc_test"/> |
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411 <expand macro="trimmomatic_test"/> |
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412 <!-- Test 10 --> |
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413 <expand macro="flexbar_test"/> |
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414 <expand macro="fastp_test"/> |
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415 <expand macro="bismark_test"/> |
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416 <expand macro="rseqc_test"/> |
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417 <expand macro="star_test"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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418 <expand macro="cutadapt_test"/> |
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419 <expand macro="samtools_test"/> |
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420 <expand macro="busco_test"/> |
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421 <expand macro="featurecounts_test"/> |
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422 <expand macro="picard_test"/> |
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423 <!-- Test 20 --> |
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424 <expand macro="qualimap_test"/> |
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425 <expand macro="gatk_test"/> |
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426 <expand macro="bamtools_test"/> |
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427 <expand macro="pycoqc_test"/> |
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428 |
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429 <!--expand macro="vcftools_test"/> Does not work, did it ever worked? --> |
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430 |
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431 </tests> |
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432 <help><![CDATA[ |
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433 **What it does** |
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434 |
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435 `MultiQC <http://multiqc.info/>`_ aggregates results from bioinformatics analyses across many samples into a single report. |
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436 It takes results of multiple analyses and creates a report that can be viewed as a single beautiful web-page. |
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437 It's a general use tool, perfect for summarizing the output from numerous bioinformatics tools. |
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438 |
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439 **Inputs** |
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440 |
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441 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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442 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 |
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443 |
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444 ]]></help> |
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445 <citations> |
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446 <citation type="doi">10.1093/bioinformatics/btw354</citation> |
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447 </citations> |
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448 <creator> |
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449 <person givenName="Cyril" familyName="Monjeaud" url="https://github.com/cmonjeau"/> |
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450 <person givenName="Yvan" familyName="Le Bras" url="https://github.com/yvanlebras"/> |
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451 <person givenName="Bérénice" familyName="Batut" url="https://github.com/bebatut"/> |
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452 <person givenName="Björn" familyName="Grüning" url="https://github.com/bgruening"/> |
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453 </creator> |
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454 </tool> |