Mercurial > repos > iuc > multiqc
annotate multiqc.xml @ 23:abfd8a6544d7 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
author | iuc |
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date | Sat, 10 Dec 2022 11:22:18 +0000 |
parents | 9a913cdee30e |
children | f7e2f1eb3a16 |
rev | line source |
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9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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1 <tool id="multiqc" name="MultiQC" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> |
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3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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2 <description>aggregate results from bioinformatics analyses into a single report</description> |
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9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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3 |
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3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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4 <macros> |
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9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
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5 <import>macros.xml</import> |
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3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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6 </macros> |
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9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
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7 <expand macro="bio_tools"/> |
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
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8 <expand macro='requirements' /> |
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e4574a4d09d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit cb4a49f04475c7f6e2d304ded739c63db9f29724
iuc
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9 <version_command>multiqc --version</version_command> |
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3bad335ccea9
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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10 <command detect_errors="aggressive"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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11 <![CDATA[ |
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e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
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12 #import re |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
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13 #import os |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
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14 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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15 die() { echo "$@" 1>&2 ; exit 1; } && |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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16 |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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17 mkdir multiqc_WDir && |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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18 |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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19 #set $configfile="F" |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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20 |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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21 #for $i, $repeat in enumerate( $results ) |
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e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
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22 #set software_dir = os.path.join('multiqc_WDir', str($repeat.software_cond.software) + '_' + str($i)) |
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3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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23 mkdir $software_dir && |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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changeset
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24 #if str($repeat.software_cond.software) == "bamtools" |
3bad335ccea9
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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25 #set $pattern = "Stats for BAM file(s)" |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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changeset
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26 @LN_FILES@ |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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27 #elif str($repeat.software_cond.software) == "bcftools" |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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28 #set $pattern = "This file was produced by bcftools stats" |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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29 @LN_FILES@ |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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30 #elif str($repeat.software_cond.software) == "bismark" |
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9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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31 @BISMARK_INPUT@ |
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3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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32 #elif str($repeat.software_cond.software) == "bowtie2" |
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5e33b465d8d5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4eb6628314458d9426ea9e6fbf6e225d93e3d0fc"
iuc
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33 #set $pattern = "% overall alignment rate" |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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34 @LN_FILES@ |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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35 #elif str($repeat.software_cond.software) == "busco" |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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36 ## Searches for files "short_summary_[samplename].txt" |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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37 #for $file in $repeat.software_cond.input |
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e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
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38 @ESCAPE_IDENTIFIER@ |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
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39 #set file_path = os.path.join($software_dir, 'short_summary_' + str($identifier)) |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
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40 ln -s '$file' '$file_path' && |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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41 #end for |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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42 #elif str($repeat.software_cond.software) == "cutadapt" |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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43 #set $pattern = "This is cutadapt" |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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44 #for $file in $repeat.software_cond.input |
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e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
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45 @ESCAPE_IDENTIFIER@ |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
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46 #set file_path = os.path.join($software_dir, str($identifier) + '.txt') |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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47 ln -s '$file' '$file_path' && |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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48 ## replace header for old cutadapt release |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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49 sed -i.old 's/You are running/This is/' '$file_path' && |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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50 grep -q "$pattern" '$file_path' || die "'$pattern' or 'You are running cutadapt' not found in the file" && |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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51 #end for |
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e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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52 #elif str($repeat.software_cond.software) == "deeptools" |
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9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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53 @DEEPTOOLS_INPUT@ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984
iuc
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54 #elif str($repeat.software_cond.software) == "fastp" |
1c2db0054039
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984
iuc
parents:
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55 #set $pattern = "report_title" |
1c2db0054039
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984
iuc
parents:
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56 #for $file in $repeat.software_cond.input |
1c2db0054039
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984
iuc
parents:
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57 @ESCAPE_IDENTIFIER@ |
1c2db0054039
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984
iuc
parents:
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58 #set file_path = os.path.join($software_dir, str($identifier) + 'fastp.json') |
1c2db0054039
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984
iuc
parents:
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59 ln -s '$file' '$file_path' && |
1c2db0054039
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984
iuc
parents:
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60 grep -q "$pattern" '$file_path' || die "'$pattern' or 'report_title' not found in the file" && |
1c2db0054039
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984
iuc
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61 #end for |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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62 #elif str($repeat.software_cond.software) == "fastqc" |
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9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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63 @FASTQC_INPUT@ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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64 #elif str($repeat.software_cond.software) == "featureCounts" |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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65 #for $file in $repeat.software_cond.input |
8
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
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66 @ESCAPE_IDENTIFIER@ |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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67 #set file_prefix = os.path.join($software_dir, str($identifier)) |
5
5746cb5cf08d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 36465d526cea3d061724952bb6cf63ee8dd069bf
iuc
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68 if grep -qw Status '$file'; then |
5746cb5cf08d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 36465d526cea3d061724952bb6cf63ee8dd069bf
iuc
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69 ln -s '$file' '${file_prefix}.summary'; |
5746cb5cf08d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 36465d526cea3d061724952bb6cf63ee8dd069bf
iuc
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70 else |
8
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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71 echo -e 'Status\t${identifier}' > '${file_prefix}.summary'; |
5
5746cb5cf08d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 36465d526cea3d061724952bb6cf63ee8dd069bf
iuc
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72 cat '$file' >> '${file_prefix}.summary'; |
5746cb5cf08d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 36465d526cea3d061724952bb6cf63ee8dd069bf
iuc
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73 fi && |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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74 #end for |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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75 #elif str($repeat.software_cond.software) == "flexbar" |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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76 #set $pattern = "flexible barcode and adapter removal" |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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77 @LN_FILES@ |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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78 #elif str($repeat.software_cond.software) == "gatk" |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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79 #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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80 #if str($repeat2.type) == "varianteval" |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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81 #set $pattern = "#:GATKTable:TiTvVariantEvaluator" |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
82 @LN_2_FILES@ |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
83 #elif str($repeat2.type) == "base_recalibrator" |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
84 #set $pattern = "#:GATKTable:Arguments:Recalibration" |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
85 @LN_2_FILES@ |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
86 #end if |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
87 #end for |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
88 #elif str($repeat.software_cond.software) == "hicup" |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
89 #for $file in $repeat.software_cond.input |
8
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
90 @ESCAPE_IDENTIFIER@ |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
91 #set file_path = os.path.join($software_dir, 'HiCUP_summary_report_' + str($identifier)) |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
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92 ln -s '${file}' '$file_path' && |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
93 #end for |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
94 #elif str($repeat.software_cond.software) == "hisat2" |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
95 #set $pattern = "HISAT2 summary stats:" |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
96 @LN_FILES@ |
6
01237d721a9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361
iuc
parents:
5
diff
changeset
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97 #elif str($repeat.software_cond.software) == "hicexplorer" |
01237d721a9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361
iuc
parents:
5
diff
changeset
|
98 #set $pattern = "Min rest. site distance" |
01237d721a9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361
iuc
parents:
5
diff
changeset
|
99 @LN_FILES@ |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
100 #elif str($repeat.software_cond.software) == "htseq" |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
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101 #set $pattern = "__too_low_aQual" |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
102 @LN_FILES@ |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
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103 #elif str($repeat.software_cond.software) == "kallisto" |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
104 #set $pattern = "finding pseudoalignments for the reads" |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
105 @LN_FILES@ |
11
f0ec41881020
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents:
10
diff
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106 #elif str($repeat.software_cond.software) == "macs2" |
f0ec41881020
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents:
10
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107 #set $pattern = "# This file is generated by MACS" |
f0ec41881020
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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108 #for $file in $repeat.software_cond.input |
f0ec41881020
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents:
10
diff
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109 @ESCAPE_IDENTIFIER@ |
f0ec41881020
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents:
10
diff
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110 #set file_path = os.path.join($software_dir, str($identifier) + '_peaks.xls') |
f0ec41881020
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents:
10
diff
changeset
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111 grep -q "$pattern" $file || die "'$pattern' not found in the file" && |
f0ec41881020
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents:
10
diff
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112 ln -s '$file' '$file_path' && |
f0ec41881020
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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113 #end for |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
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114 #elif str($repeat.software_cond.software) == "picard" |
22
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
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115 @PICCARD_INPUT@ |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
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116 #elif str($repeat.software_cond.software) == "prokka" |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
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117 #set $pattern = "contigs:" |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
118 @LN_FILES@ |
21
75c93c70d094
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
iuc
parents:
20
diff
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119 #elif str($repeat.software_cond.software) == "pycoqc" |
75c93c70d094
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
iuc
parents:
20
diff
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120 #set $pattern = "\"pycoqc\":" |
75c93c70d094
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
iuc
parents:
20
diff
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|
121 @LN_FILES@ |
16
bf675f34b056
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875"
iuc
parents:
15
diff
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122 #elif str($repeat.software_cond.software) == "qualimap" |
22
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
123 @QUALIMAP_INPUT@ |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
124 #elif str($repeat.software_cond.software) == "quast" |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
125 #for $k, $file in enumerate($repeat.software_cond.input) |
8
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
126 #set file_dir = os.path.join($software_dir, 'file_' + str($k)) |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
127 #set file_path = os.path.join($file_dir, 'report.tsv') |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
128 mkdir '$file_dir' && |
8
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
129 ln -s '$file' '$file_path' && |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
130 #end for |
3bad335ccea9
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) == "rsem" |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
132 #for $file in $repeat.software_cond.input |
8
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
133 @ESCAPE_IDENTIFIER@ |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
134 #set file_path = os.path.join($software_dir, str($identifier) + '.cnt') |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
135 ln -s '$file' '$file_path' && |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
136 #end for |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
137 #elif str($repeat.software_cond.software) == "rseqc" |
22
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
138 @RSEQ_INPUT@ |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
139 #elif str($repeat.software_cond.software) == "salmon" |
22
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
140 @SALMON_INPUT@ |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
141 #elif str($repeat.software_cond.software) == "samblaster" |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
142 #set $pattern = "samblaster: Version" |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
143 @LN_FILES@ |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
144 #elif str($repeat.software_cond.software) == "samtools" |
22
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
145 @SAMTOOLS_INPUT@ |
13
161f4383df15
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b
iuc
parents:
12
diff
changeset
|
146 #elif str($repeat.software_cond.software) == "slamdunk" |
161f4383df15
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b
iuc
parents:
12
diff
changeset
|
147 #set $pattern = "# slamdunk" |
161f4383df15
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b
iuc
parents:
12
diff
changeset
|
148 @LN_FILES@ |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
149 #elif str($repeat.software_cond.software) == "snpeff" |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
150 #set $pattern = "SnpEff_version" |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
151 @LN_FILES@ |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
152 #elif str($repeat.software_cond.software) == "sortmerna" |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
153 #set $pattern = "Minimal SW score based on E-value" |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
154 @LN_FILES@ |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
155 #else if str($repeat.software_cond.software) == "star": |
22
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
156 @STAR_INPUT@ |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
157 #elif str($repeat.software_cond.software) == "tophat" |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
158 #for $file in $repeat.software_cond.input |
8
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
159 @ESCAPE_IDENTIFIER@ |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
160 #set file_path = os.path.join($software_dir, str($identifier) + 'align_summary.txt') |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
161 ln -s '$file' '$file_path' && |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
162 #end for |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
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|
163 #elif str($repeat.software_cond.software) == "trimmomatic" |
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164 #set $pattern = "Trimmomatic" |
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165 @LN_FILES@ |
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166 #elif str($repeat.software_cond.software) == "vcftools" |
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167 @VCFTOOLS_INPUT@ |
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168 #else if str($repeat.software_cond.software) == "custom_content": |
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169 #set $configfile = "T" |
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170 #for $j, $file in enumerate( $repeat.software_cond.input ) |
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171 #set file_path = os.path.join($software_dir, 'file_' + str($i) + '_' + str($j)) |
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172 ln -s '$file' '$file_path' && |
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173 more $file && |
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174 #end for |
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175 #end if |
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176 #end for |
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177 |
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178 multiqc multiqc_WDir |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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179 --filename 'report' |
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180 |
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181 #if str($title) |
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182 --title '$title' |
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183 #end if |
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184 #if str($comment) |
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185 --comment '$comment' |
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186 #end if |
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187 |
15
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188 $flat |
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189 $export |
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190 |
0
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191 #if $configfile == "T" |
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192 --config '$multiqc_config' |
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193 #end if |
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194 ]]></command> |
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195 <configfiles> |
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196 <configfile name="multiqc_config"> |
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197 <![CDATA[ |
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198 custom_data: |
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199 #for $i, $repeat in enumerate( $results ) |
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200 #if str($repeat.software_cond.software) == "custom_content" |
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201 section_$i: |
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202 file_format: 'tsv' |
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203 section_name: '$repeat.software_cond.section_name' |
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204 title: '$repeat.software_cond.title' |
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205 description: '$repeat.software_cond.description' |
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206 plot_type: '$repeat.software_cond.plot_type' |
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207 pconfig: |
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208 id: 'section_${i}_${repeat.software_cond.plot_type}' |
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209 ylab: '$repeat.software_cond.ylab' |
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210 xlab: '$repeat.software_cond.xlab' |
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211 #end if |
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212 #end for |
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213 sp: |
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214 #for $i, $repeat in enumerate( $results ) |
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215 #if str($repeat.software_cond.software) == "custom_content" |
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216 section_$i: |
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217 fn: 'file_${i}_*' |
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218 #end if |
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219 #end for |
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220 ]]></configfile> |
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221 </configfiles> |
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222 <inputs> |
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223 <repeat name="results" title="Results" min="1"> |
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224 <conditional name="software_cond"> |
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225 <param name="software" type="select" label="Which tool was used generate logs?" help="Software name"> |
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226 <!--<option value="adapterRemoval">Adapter Removal</option>--> |
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227 <!--<option value="afterqc">AfterQC</option>--> |
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228 <option value="bamtools">Bamtools</option> |
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229 <!--<option value="bbmap">BBMap</option>--> |
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230 <option value="bcftools">Bcftools</option> |
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231 <!--<option value="bcl2fastq">bcl2fastq</option>--> |
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232 <!--<option value="biobambam2">biobambam2</option>--> |
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233 <!--<option value="biobloomtools">BioBloom Tools</option>--> |
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234 <option value="bismark">Bismark</option> |
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235 <!--<option value="bowtie1">Bowtie 1</option>--> |
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236 <option value="bowtie2">Bowtie 2</option> |
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237 <option value="busco">BUSCO</option> |
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238 <!--<option value="clusterflow">Cluster Flow</option>--> |
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239 <option value="cutadapt">Cutadapt/Trim Galore!</option> |
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240 <!--<option value="clipandmerge">ClipAndMerge</option>--> |
0
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241 <!--<option value="conpair">Conpair</option>--> |
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242 <!--<option value="dedup">DeDup</option>--> |
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243 <option value="deeptools">deepTools</option> |
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244 <!--<option value="disambiguate">Disambiguate</option>--> |
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245 <!--<option value="fastq_screen">FastQ Screen</option>--> |
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246 <option value="fastp">fastp</option> |
0
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247 <option value="fastqc">FastQC</option> |
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248 <option value="featureCounts">featureCounts</option> |
16
bf675f34b056
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875"
iuc
parents:
15
diff
changeset
|
249 <!--<option value="fgbio">fgbio</option>--> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
250 <option value="flexbar">Flexbar</option> |
8
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
251 <option value="gatk">GATK</option> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
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|
252 <!--<option value="goleft_indexcov">goleft indexcov</option>--> |
6
01237d721a9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361
iuc
parents:
5
diff
changeset
|
253 <option value="hicexplorer">HiCExplorer</option> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
254 <!--<option value="hicup">HiCUP</option>--> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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changeset
|
255 <option value="hisat2">HISAT2</option> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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changeset
|
256 <!--<option value="homer">HOMER</option>--> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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changeset
|
257 <option value="htseq">HTSeq</option> |
8
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
258 <!--<option value="interop">InterOp</option>--> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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changeset
|
259 <!--<option value="jellyfish">Jellyfish</option>--> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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changeset
|
260 <option value="kallisto">Kallisto</option> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
261 <!--<option value="leehom">leeHom</option>--> |
11
f0ec41881020
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents:
10
diff
changeset
|
262 <option value="macs2">MACS2</option> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
263 <!--<option value="methylQA">methylQA</option>--> |
16
bf675f34b056
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875"
iuc
parents:
15
diff
changeset
|
264 <!--<option value="mosdepth">mostdepth</option>--> |
bf675f34b056
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875"
iuc
parents:
15
diff
changeset
|
265 <!--<option value="mtnucratio">mtnucratio</option>--> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
266 <!--<option value="peddy">Peddy</option>--> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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changeset
|
267 <option value="picard">Picard</option> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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changeset
|
268 <!--<option value="preseq">Preseq</option>--> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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|
269 <option value="prokka">Prokka</option> |
21
75c93c70d094
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
iuc
parents:
20
diff
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|
270 <option value="pycoqc">PycoQC</option> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
271 <!--<option value="qorts">QoRTs</option>--> |
16
bf675f34b056
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875"
iuc
parents:
15
diff
changeset
|
272 <option value="qualimap">Qualimap (BamQC or RNASeq output)</option> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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|
273 <option value="quast">QUAST</option> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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|
274 <!--<option value="rna_seqc">RNA-SeQC</option>--> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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|
275 <!--<option value="rsem">RSEM (rsem-calculate-regex output)</option>--> |
8
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
276 <option value="rseqc">RSeQC</option> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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changeset
|
277 <!--<option value="salmon">Salmon</option>--> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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|
278 <option value="samblaster">Samblaster</option> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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|
279 <option value="samtools">Samtools</option> |
8
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
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|
280 <!--<option value="sargasso">Sargasso</option>--> |
16
bf675f34b056
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875"
iuc
parents:
15
diff
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|
281 <!--<option value="seqyclean">SeqyClean</option>--> |
bf675f34b056
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875"
iuc
parents:
15
diff
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|
282 <!--<option value="sexdeterrmine">SexDetErrmine</option>--> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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|
283 <!--<option value="skewer">Skewer</option>--> |
13
161f4383df15
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b
iuc
parents:
12
diff
changeset
|
284 <option value="slamdunk">Slamdunk</option> |
8
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
285 <option value="snpeff">SnpEff</option> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
286 <option value="sortmerna">SortMeRNA</option> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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287 <option value="star">STAR</option> |
8
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
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|
288 <!--<option value="supernova">Supernova</option>--> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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|
289 <!--<option value="theta2">THeTA2</option>--> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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|
290 <option value="tophat">TopHat2</option> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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|
291 <option value="trimmomatic">Trimmomatic</option> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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|
292 <option value="vcftools">VCFTools</option> |
8
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
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|
293 <!--<option value="verifybamid">VerifyBAMID</option>--> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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294 <!--Custom--> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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|
295 <option value="custom_content">Custom Content</option> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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changeset
|
296 </param> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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changeset
|
297 <when value="bamtools"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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|
298 <param name="input" type="data" format="txt" multiple="true" label="Output of BAMtools" help="It should contain 'Stats for BAM file(s)'"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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299 </when> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
300 <when value="bcftools"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
301 <param name="input" type="data" format="txt" multiple="true" label="Output of BAMtools" help="It should contain 'This file was produced by bcftools stats'"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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|
302 </when> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
303 <when value="bismark"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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|
304 <repeat name="output" title="Bismark output" min="1"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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|
305 <param name="type" type="select" label="Type of Bismark output?"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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|
306 <option value="align">Alignment file</option> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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|
307 <option value="dedup">Deduplication file</option> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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|
308 <option value="meth_extract">Methylation file</option> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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|
309 <option value="m_bias">m_bias file</option> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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|
310 <option value="bam2nuc">bam2nuc file</option> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
311 </param> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
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|
312 <param name="input" type="data" format="txt" multiple="true" label="Bismark output"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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changeset
|
313 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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changeset
|
314 </when> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
315 <when value="bowtie2"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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|
316 <param name="input" type="data" format="txt" multiple="true" label="Output of Bowtie 2" help="It should contain 'reads; of these:'"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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changeset
|
317 </when> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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|
318 <when value="busco"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
319 <param name="input" type="data" format="txt" multiple="true" label="Output of BUSCO"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
320 </when> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
321 <when value="cutadapt"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
322 <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of Cutadapt" help="It should contain 'This is cutadapt' or 'You are running cutadapt'"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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|
323 </when> |
8
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
324 <when value="deeptools"> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
325 <repeat name="output" title="deepTools output" min="1"> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
326 <param name="type" type="select" label="deepTool used to generate the output?"> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
327 <option value="bamPEFragmentSize">bamPEFragmentSize</option> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
328 <option value="estimateReadFiltering">estimateReadFiltering</option> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
329 <option value="plotCoverageStdout">plotCoverageStdout</option> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
330 <option value="plotCoverageOutRawCounts">plotCoverageOutRawCounts</option> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
331 <option value="plotEnrichment">plotEnrichment</option> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
332 <option value="plotFingerprintOutRawCounts">plotFingerprintOutRawCounts</option> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
333 <option value="plotFingerprintOutQualityMetrics">plotFingerprintOutQualityMetrics</option> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
334 </param> |
e0f4a651c6b9
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="txt" multiple="true" label="Bismark output"/> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
336 </repeat> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
337 </when> |
12
1c2db0054039
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984
iuc
parents:
11
diff
changeset
|
338 <when value="fastp"> |
1c2db0054039
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984
iuc
parents:
11
diff
changeset
|
339 <param name="input" type="data" format="json" multiple="true" label="Output of fastp" help="It should be the json report from fastp containing 'report_title'"/> |
1c2db0054039
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984
iuc
parents:
11
diff
changeset
|
340 </when> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
341 <when value="fastqc"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
342 <repeat name="output" title="FastQC output" min="1"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
343 <param name="type" type="select" label="Type of FastQC output?"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
344 <option value="data">Raw data</option> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
345 <option value="theoretical_gc">Theorectical GC</option> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
346 </param> |
8
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
347 <param name="input" type="data" format="txt" multiple="true" label="FastQC output"> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
348 <validator type="expression" message="MultiQC does not accept the HTML report generated by FastQC, only the Raw Data">value is not None and value.extension != "html"</validator> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
349 </param> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
350 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
351 </when> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
352 <when value="featureCounts"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
353 <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of FeatureCounts"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
354 </when> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
355 <when value="flexbar"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
356 <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of Flexbar" help="It should contain 'Flexbar - flexible barcode and adapter removal'"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
357 </when> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
358 <when value="gatk"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
359 <repeat name="output" title="GATK output" min="1"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
360 <param name="type" type="select" label="Type of GATK output?"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
361 <option value="varianteval">Variant eval file</option> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
362 <option value="base_recalibrator">Base recalibrator file</option> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
363 </param> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
364 <param name="input" type="data" format="txt" multiple="true" label="GATK output"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
365 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
366 </when> |
6
01237d721a9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361
iuc
parents:
5
diff
changeset
|
367 <when value="hicexplorer"> |
01237d721a9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361
iuc
parents:
5
diff
changeset
|
368 <param name="input" type="data" format="txt,tabular" multiple="true" label="Output of HiCExplorer" help="It should contain 'Min rest. site distance'"/> |
01237d721a9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361
iuc
parents:
5
diff
changeset
|
369 </when> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
370 <when value="hisat2"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
371 <param name="input" type="data" format="txt,tabular" multiple="true" label="Output of HISAT2" help="It should contain 'HISAT2 summary stats:'"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
372 </when> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
373 <when value="htseq"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
374 <param name="input" type="data" format="txt,tabular" multiple="true" label="Output of HTSeq" help="It should contain '__too_low_aQual'"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
375 </when> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
376 <when value="kallisto"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
377 <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of Kallisto" help="It should contain '[quant] finding pseudoalignments for the reads'"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
378 </when> |
11
f0ec41881020
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents:
10
diff
changeset
|
379 <when value="macs2"> |
f0ec41881020
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents:
10
diff
changeset
|
380 <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'"/> |
f0ec41881020
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents:
10
diff
changeset
|
381 </when> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
382 <when value="picard"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
383 <repeat name="output" title="Picard output" min="1"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
384 <param name="type" type="select" label="Type of Picard output?"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
385 <option value="alignment_metrics">Alignment metrics</option> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
386 <option value="basedistributionbycycle">Base distribution by cycle</option> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
387 <option value="gcbias">GC bias</option> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
388 <option value="hsmetrics">HS Metrics</option> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
389 <option value="insertsize">Insert size</option> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
390 <option value="markdups">Markdups</option> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
391 <option value="oxogmetrics">Oxog metrics</option> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
392 <option value="pcr_metrics">PCR metrics</option> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
393 <option value="rnaseqmetrics">RNA Seq metrics</option> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
394 <option value="rrbs_metrics">RRBS metrics</option> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
395 <option value="wgs_metrics">WGS metrics</option> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
396 </param> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
397 <param name="input" type="data" format="txt" multiple="true" label="Picard output"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
398 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
399 </when> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
400 <when value="prokka"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
401 <param name="input" type="data" format="txt" multiple="true" label="Output of Prokka" help="It should contain 'contigs:'"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
402 </when> |
21
75c93c70d094
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
iuc
parents:
20
diff
changeset
|
403 <when value="pycoqc"> |
75c93c70d094
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
iuc
parents:
20
diff
changeset
|
404 <param name="input" type="data" format="txt,json" multiple="true" label="Output of PycoQC"/> |
75c93c70d094
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
iuc
parents:
20
diff
changeset
|
405 </when> |
16
bf675f34b056
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875"
iuc
parents:
15
diff
changeset
|
406 <when value="qualimap"> |
bf675f34b056
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875"
iuc
parents:
15
diff
changeset
|
407 <param name="input" type="data" format="txt,tabular,tsv" multiple="true" label="Output of Qualimap BamQC" help="First result input should be genome_coverage (default from tool output). Run the Flatten Collection tool to keep all output in one report" /> |
bf675f34b056
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875"
iuc
parents:
15
diff
changeset
|
408 </when> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
409 <when value="quast"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
410 <param name="input" type="data" format="tabular,tsv" multiple="true" label="Output of Quast"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
411 </when> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
412 <when value="rseqc"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
413 <repeat name="output" title="RSeQC output" min="1"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
414 <conditional name="type"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
415 <param name="type" type="select" label="Type of RSeQC output?"> |
23
abfd8a6544d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents:
22
diff
changeset
|
416 <option value="bam_stat">BAM/SAM mapping stats</option> |
abfd8a6544d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents:
22
diff
changeset
|
417 <option value="gene_body_coverage">Gene body coverage</option> |
abfd8a6544d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents:
22
diff
changeset
|
418 <option value="infer_experiment">Infer experiment</option> |
abfd8a6544d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents:
22
diff
changeset
|
419 <option value="inner_distance">Inner distance</option> |
abfd8a6544d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents:
22
diff
changeset
|
420 <option value="junction_annotation">Junction annotation</option> |
abfd8a6544d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents:
22
diff
changeset
|
421 <option value="junction_saturation">Junction saturation</option> |
abfd8a6544d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents:
22
diff
changeset
|
422 <option value="read_distribution">Read distribution</option> |
abfd8a6544d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents:
22
diff
changeset
|
423 <option value="read_duplication_pos">Read duplication</option> |
abfd8a6544d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents:
22
diff
changeset
|
424 <option value="read_gc">Read GC</option> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
425 </param> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
426 <when value="bam_stat"> |
23
abfd8a6544d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents:
22
diff
changeset
|
427 <param name="input" type="data" format="txt,tabular" multiple="true" label="RSeQC BAM stat: output file" help="It should contain 'Proper-paired reads map to different chrom:'"/> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
428 </when> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
429 <when value="gene_body_coverage"> |
23
abfd8a6544d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents:
22
diff
changeset
|
430 <param name="input" type="data" format="txt" multiple="true" label="RSeQC gene body coverage: stats file"/> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
431 </when> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
432 <when value="infer_experiment"> |
23
abfd8a6544d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents:
22
diff
changeset
|
433 <param name="input" type="data" format="txt" multiple="true" label="RSeQC infer experiment: configuration output" help="It should contain 'Fraction of reads explained by'"/> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
434 </when> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
435 <when value="inner_distance"> |
23
abfd8a6544d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents:
22
diff
changeset
|
436 <param name="input" type="data" format="txt" multiple="true" label="RSeQC inner distance: frequency file"/> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
437 </when> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
438 <when value="junction_annotation"> |
23
abfd8a6544d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents:
22
diff
changeset
|
439 <param name="input" type="data" format="txt" multiple="true" label="RSeQC junction annotation: stats file" help="It should contain 'Partial Novel Splicing Junctions:'"/> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
440 </when> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
441 <when value="junction_saturation"> |
23
abfd8a6544d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents:
22
diff
changeset
|
442 <param name="input" type="data" format="txt" multiple="true" label="RSeQC junction saturation: junction saturation plot Rscript file"/> |
1
6999173dc0c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 110247de01764a544371d07eaed0308429a47daa
iuc
parents:
0
diff
changeset
|
443 </when> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
444 <when value="read_distribution"> |
23
abfd8a6544d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents:
22
diff
changeset
|
445 <param name="input" type="data" format="txt" multiple="true" label="RSeQC read distribution: stats output" help="It should contain 'Group Total_bases Tag_count Tags/Kb'"/> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
446 </when> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
447 <when value="read_duplication_pos"> |
23
abfd8a6544d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents:
22
diff
changeset
|
448 <param name="input" type="data" format="xls" multiple="true" label="RSeQC read duplication: positions XLS file"/> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
449 </when> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
450 <when value="read_gc"> |
23
abfd8a6544d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents:
22
diff
changeset
|
451 <param name="input" type="data" format="csv,xls,tabular" multiple="true" label="RSeQC read GC output"/> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
452 </when> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
453 </conditional> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
454 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
455 </when> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
456 <when value="samblaster"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
457 <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of Samblaster" help="It should contain 'samblaster: Version'"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
458 </when> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
459 <when value="samtools"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
460 <repeat name="output" title="Samtools output" min="1"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
461 <conditional name="type"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
462 <param name="type" type="select" label="Type of Samtools output?"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
463 <option value="stats">stats</option> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
464 <option value="flagstat">flagstat</option> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
465 <option value="idxstats">idxstats</option> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
466 <option value="rmdup">rmdup</option> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
467 </param> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
468 <when value="stats"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
469 <param name="input" type="data" format="txt" multiple="true" label="Samtools stats output" help="It should contain 'This file was produced by samtools stats'"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
470 </when> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
471 <when value="flagstat"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
472 <param name="input" type="data" format="txt" multiple="true" label="Samtools flagstat output" help="It should contain 'in total (QC-passed reads + QC-failed reads)'"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
473 </when> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
474 <when value="idxstats"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
475 <param name="input" type="data" format="txt" multiple="true" label="Samtools idxstats output"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
476 </when> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
477 <when value="rmdup"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
478 <param name="input" type="data" format="txt" multiple="true" label="Samtools rmdup output" help="It should contain '[bam_rmdup'"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
479 </when> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
480 </conditional> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
481 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
482 </when> |
13
161f4383df15
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b
iuc
parents:
12
diff
changeset
|
483 <when value="slamdunk"> |
161f4383df15
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b
iuc
parents:
12
diff
changeset
|
484 <param name="input" type="data" format="txt,tabular" multiple="true" label="Output of Slamdunk Alleyoop" help="It should contain '# slamdunk'"/> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
485 </when> |
8
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
486 <when value="snpeff"> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
487 <param name="input" type="data" format="csv" multiple="true" label="Output of SnpEff"/> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
488 </when> |
13
161f4383df15
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b
iuc
parents:
12
diff
changeset
|
489 <when value="sortmerna"> |
161f4383df15
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b
iuc
parents:
12
diff
changeset
|
490 <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'"/> |
161f4383df15
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b
iuc
parents:
12
diff
changeset
|
491 </when> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
492 <when value="star"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
493 <repeat name="output" title="STAR output" min="1"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
494 <conditional name="type"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
495 <param name="type" type="select" label="Type of STAR output?"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
496 <option value="log">Log</option> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
497 <option value="genecounts">Gene counts</option> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
498 </param> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
499 <when value="log"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
500 <param name="input" type="data" format="txt" multiple="true" label="STAR log output"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
501 </when> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
502 <when value="genecounts"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
503 <param name="input" type="data" format="tabular,tsv" multiple="true" label="STAR gene count output"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
504 </when> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
505 </conditional> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
506 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
507 </when> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
508 <when value="tophat"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
509 <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of TopHat2"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
510 </when> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
511 <when value="trimmomatic"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
512 <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of Trimmomatic" help="It should contain 'TTrimmomatic'"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
513 </when> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
514 <when value="vcftools"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
515 <repeat name="output" title="VCFTools output" min="1"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
516 <conditional name="type"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
517 <param name="type" type="select" label="Type of VCFTools output?"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
518 <option value="relatedness2">relatedness2</option> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
519 <option value="tstv_by_count">tstv_by_count</option> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
520 <option value="tstv_by_qual">tstv_by_qual</option> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
521 <option value="tstv_summary">tstv_summary</option> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
522 </param> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
523 <when value="relatedness2"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
524 <param name="input" type="data" format="txt" multiple="true" label="VCFTools relatedness2 output"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
525 </when> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
526 <when value="tstv_by_count"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
527 <param name="input" type="data" format="tabular,tsv" multiple="true" label="VCFTools TsTV count output"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
528 </when> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
529 <when value="tstv_by_qual"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
530 <param name="input" type="data" format="tabular" multiple="true" label="VCFTools TsTV qual output"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
531 </when> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
532 <when value="tstv_summary"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
533 <param name="input" type="data" format="txt" multiple="true" label="VCFTools TsTV summary output"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
534 </when> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
535 </conditional> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
536 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
537 </when> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
538 <when value="custom_content"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
539 <param argument="plot_type" label="The plot type to visualise the data with" type="select"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
540 <option value="linegraph">linegraph</option> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
541 <option value="bargraph">bargraph</option> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
542 <option value="scatter">scatter</option> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
543 <option value="generalstats">generalstats</option> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
544 <option value="table">table</option> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
545 </param> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
546 <param argument="section_name" label="Section name" type="text" help="Nice name used for the report section header" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
547 <param argument="title" label="Title" type="text" help="Plot title" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
548 <param argument="description" label="Description" type="text" help="Introductory text to be printed under the section header" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
549 <param argument="xlab" label="X axis label" type="text" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
550 <param argument="ylab" label="Y axis label" type="text" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
551 <param name="input" type="data" format="tabular,tsv" multiple="true" label="Data files"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
552 </when> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
553 </conditional> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
554 </repeat> |
22
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
555 <param name="title" type="text" value="" optional="true" label="Report title" help="It is printed as page header"> |
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
556 <sanitizer invalid_char=""> |
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
557 <valid initial="string.letters,string.digits"> |
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
558 <add value="," /> |
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
559 <add value=":" /> |
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
560 <add value="-" /> |
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
561 <add value="_" /> |
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
562 <add value=" " /> |
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
563 <add value="." /> |
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
564 </valid> |
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
565 </sanitizer> |
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
566 <validator type="regex">[0-9a-zA-Z,: _.-]+</validator> |
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
567 </param> |
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
568 <param name="comment" type="text" value="" optional="true" label="Custom comment" help="It will be printed at the top of the report"> |
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
569 <sanitizer invalid_char=""> |
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
570 <valid initial="string.letters,string.digits"> |
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
571 <add value="," /> |
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
572 <add value=":" /> |
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
573 <add value="-" /> |
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
574 <add value="_" /> |
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
575 <add value=" " /> |
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
576 <add value="." /> |
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
577 </valid> |
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
578 </sanitizer> |
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
579 <validator type="regex">[0-9a-zA-Z,: _.-]+</validator> |
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
580 </param> |
18
c19b16e5729c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 263b1803fbf2622dbeb283b1d965690a5dc24ec9"
iuc
parents:
17
diff
changeset
|
581 <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."/> |
19
f7985e0479b9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 2b946616b7d12eed507d95ebbd8fd257ae37d83b"
iuc
parents:
18
diff
changeset
|
582 <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"/> |
18
c19b16e5729c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 263b1803fbf2622dbeb283b1d965690a5dc24ec9"
iuc
parents:
17
diff
changeset
|
583 <param name="saveLog" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output the multiQC log file?" help="This is mostly useful for debugging purposes"/> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
584 </inputs> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
585 <outputs> |
8
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
586 <data name="html_report" format="html" from_work_dir="report.html" label="${tool.name} on ${on_string}: Webpage" /> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
587 <data name="log" format="txt" from_work_dir="report_data/multiqc.log" label="${tool.name} on ${on_string}: Log"> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
588 <filter>saveLog</filter> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
589 </data> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
590 <collection name="stats" type="list" label="${tool.name} on ${on_string}: Stats"> |
8
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
591 <discover_datasets pattern="multiqc_(?P<designation>.+)\.txt" format="tabular" directory="report_data" /> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
592 </collection> |
15
3d93dd18d9f8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6"
iuc
parents:
13
diff
changeset
|
593 <collection name="plots" type="list" label="${tool.name} on ${on_string}: Plots"> |
18
c19b16e5729c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 263b1803fbf2622dbeb283b1d965690a5dc24ec9"
iuc
parents:
17
diff
changeset
|
594 <discover_datasets pattern="mqc_(?P<designation>.+)\.txt" format="tabular" directory="report_data" /> |
19
f7985e0479b9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 2b946616b7d12eed507d95ebbd8fd257ae37d83b"
iuc
parents:
18
diff
changeset
|
595 <filter>export</filter> |
15
3d93dd18d9f8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6"
iuc
parents:
13
diff
changeset
|
596 </collection> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
597 </outputs> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
598 <tests> |
22
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
599 <!--Test 01--> |
18
c19b16e5729c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 263b1803fbf2622dbeb283b1d965690a5dc24ec9"
iuc
parents:
17
diff
changeset
|
600 <test expect_num_outputs="4"> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
601 <repeat name="results"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
602 <conditional name="software_cond"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
603 <param name="software" value="cutadapt" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
604 <param name="input" value="cutadapt.txt" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
605 </conditional> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
606 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
607 <repeat name="results"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
608 <conditional name="software_cond"> |
12
1c2db0054039
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984
iuc
parents:
11
diff
changeset
|
609 <param name="software" value="fastp" /> |
1c2db0054039
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984
iuc
parents:
11
diff
changeset
|
610 <param name="input" value="fastp1.json.txt,fastp2.json.txt" /> |
1c2db0054039
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984
iuc
parents:
11
diff
changeset
|
611 </conditional> |
1c2db0054039
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984
iuc
parents:
11
diff
changeset
|
612 </repeat> |
1c2db0054039
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984
iuc
parents:
11
diff
changeset
|
613 <repeat name="results"> |
1c2db0054039
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984
iuc
parents:
11
diff
changeset
|
614 <conditional name="software_cond"> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
615 <param name="software" value="fastqc" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
616 <repeat name="output"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
617 <param name="type" value="data"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
618 <param name="input" value="fastqc_1.txt,fastqc_2.txt"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
619 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
620 </conditional> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
621 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
622 <repeat name="results"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
623 <conditional name="software_cond"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
624 <param name="software" value="flexbar" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
625 <param name="input" value="flexbar.txt" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
626 </conditional> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
627 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
628 <repeat name="results"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
629 <conditional name="software_cond"> |
13
161f4383df15
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b
iuc
parents:
12
diff
changeset
|
630 <param name="software" value="slamdunk" /> |
161f4383df15
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b
iuc
parents:
12
diff
changeset
|
631 <param name="input" value="slamdunk_summary.txt,slamdunk_reads1_overallrates.csv,slamdunk_reads2_overallrates.csv" /> |
161f4383df15
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b
iuc
parents:
12
diff
changeset
|
632 </conditional> |
161f4383df15
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b
iuc
parents:
12
diff
changeset
|
633 </repeat> |
161f4383df15
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b
iuc
parents:
12
diff
changeset
|
634 <repeat name="results"> |
161f4383df15
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b
iuc
parents:
12
diff
changeset
|
635 <conditional name="software_cond"> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
636 <param name="software" value="sortmerna" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
637 <param name="input" value="sortmerna.txt" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
638 </conditional> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
639 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
640 <repeat name="results"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
641 <conditional name="software_cond"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
642 <param name="software" value="trimmomatic" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
643 <param name="input" value="trimmomatic.txt" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
644 </conditional> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
645 </repeat> |
8
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
646 <param name="title" value="Title of the report"/> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
647 <param name="comment" value="Commment for the report"/> |
18
c19b16e5729c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 263b1803fbf2622dbeb283b1d965690a5dc24ec9"
iuc
parents:
17
diff
changeset
|
648 <param name="flat" value="true"/> |
19
f7985e0479b9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 2b946616b7d12eed507d95ebbd8fd257ae37d83b"
iuc
parents:
18
diff
changeset
|
649 <param name="export" value="true"/> |
18
c19b16e5729c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 263b1803fbf2622dbeb283b1d965690a5dc24ec9"
iuc
parents:
17
diff
changeset
|
650 <param name="saveLog" value="true"/> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
651 <output name="html_report"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
652 <assert_contents> |
8
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
653 <has_text text="Title of the report" /> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
654 <has_text text="Commment for the report" /> |
19
f7985e0479b9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 2b946616b7d12eed507d95ebbd8fd257ae37d83b"
iuc
parents:
18
diff
changeset
|
655 <has_text text="cutadapt_trimmed_sequences_plot" /> |
12
1c2db0054039
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984
iuc
parents:
11
diff
changeset
|
656 <has_text text="An ultra-fast all-in-one FASTQ preprocessor" /> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
657 <has_text text="fastqc_seq_heatmap_key_t" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
658 <has_text text="flexbar_plot" /> |
13
161f4383df15
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b
iuc
parents:
12
diff
changeset
|
659 <has_text text="a tool to analyze SLAMSeq data" /> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
660 <has_text text="sortmerna-detailed-plot" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
661 <has_text text="trimmomatic_plot" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
662 </assert_contents> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
663 </output> |
18
c19b16e5729c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 263b1803fbf2622dbeb283b1d965690a5dc24ec9"
iuc
parents:
17
diff
changeset
|
664 <output name="log"> |
c19b16e5729c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 263b1803fbf2622dbeb283b1d965690a5dc24ec9"
iuc
parents:
17
diff
changeset
|
665 <assert_contents> |
c19b16e5729c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 263b1803fbf2622dbeb283b1d965690a5dc24ec9"
iuc
parents:
17
diff
changeset
|
666 <has_text_matching expression="\[INFO \] MultiQC complete$"/> |
c19b16e5729c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 263b1803fbf2622dbeb283b1d965690a5dc24ec9"
iuc
parents:
17
diff
changeset
|
667 </assert_contents> |
c19b16e5729c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 263b1803fbf2622dbeb283b1d965690a5dc24ec9"
iuc
parents:
17
diff
changeset
|
668 </output> |
19
f7985e0479b9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 2b946616b7d12eed507d95ebbd8fd257ae37d83b"
iuc
parents:
18
diff
changeset
|
669 <output_collection name="stats" type="list" count="10"> |
22
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
670 <expand macro="element_assert" name="cutadapt" columns="9" lines="2" text="dataset_33"/> |
20
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
671 <expand macro="element_assert" name="fastp" columns="2" lines="3" text="R1_fq"/> |
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
672 <expand macro="element_assert" name="fastqc" columns="22" lines="3" text="poulet5_1"/> |
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
673 <expand macro="element_assert" name="flexbar" columns="11" lines="2" text="result_right"/> |
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
674 <expand macro="element_assert" name="general_stats" columns="20" lines="11" text="bwa-mem-fastq1_fq"/> |
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
675 <expand macro="element_assert" name="slamdunk_readrates_plus" columns="13" lines="3" text="slamdunk_reads1_overallrates_csv"/> |
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
676 <expand macro="element_assert" name="slamdunk_readrates_minus" columns="13" lines="3" text="slamdunk_reads1_overallrates_csv"/> |
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
677 <expand macro="element_assert" name="sortmerna" columns="22" lines="2" text="25839_merged"/> |
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
678 <expand macro="element_assert" name="sources" columns="4" lines="7" text="Module"/> |
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
679 <expand macro="element_assert" name="trimmomatic" columns="6" lines="2" text="C2"/> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
680 </output_collection> |
18
c19b16e5729c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 263b1803fbf2622dbeb283b1d965690a5dc24ec9"
iuc
parents:
17
diff
changeset
|
681 <output_collection name="plots" type="list" count="29"/> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
682 </test> |
22
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
683 <!--Test 02--> |
18
c19b16e5729c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 263b1803fbf2622dbeb283b1d965690a5dc24ec9"
iuc
parents:
17
diff
changeset
|
684 <test expect_num_outputs="2"> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
685 <repeat name="results"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
686 <conditional name="software_cond"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
687 <param name="software" value="bismark" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
688 <repeat name="output"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
689 <param name="type" value="align"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
690 <param name="input" value="bismark.txt"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
691 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
692 </conditional> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
693 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
694 <repeat name="results"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
695 <conditional name="software_cond"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
696 <param name="software" value="bowtie2" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
697 <param name="input" value="bowtie2_1.txt,bowtie2_2.txt" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
698 </conditional> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
699 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
700 <repeat name="results"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
701 <conditional name="software_cond"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
702 <param name="software" value="hisat2" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
703 <param name="input" value="hisat2_1.txt,hisat2_2.txt" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
704 </conditional> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
705 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
706 <repeat name="results"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
707 <conditional name="software_cond"> |
6
01237d721a9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361
iuc
parents:
5
diff
changeset
|
708 <param name="software" value="hicexplorer" /> |
9
df99138d2776
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 31d721c19f5681dfe542dd23185c06c8f29f1945
iuc
parents:
8
diff
changeset
|
709 <param name="input" value="hicexplorer1.log,hicexplorer1.log,hicexplorer2.log" /> |
6
01237d721a9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361
iuc
parents:
5
diff
changeset
|
710 </conditional> |
01237d721a9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361
iuc
parents:
5
diff
changeset
|
711 </repeat> |
01237d721a9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361
iuc
parents:
5
diff
changeset
|
712 <repeat name="results"> |
01237d721a9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361
iuc
parents:
5
diff
changeset
|
713 <conditional name="software_cond"> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
714 <param name="software" value="kallisto" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
715 <param name="input" value="kallisto_1.txt,kallisto_2.txt" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
716 </conditional> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
717 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
718 <repeat name="results"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
719 <conditional name="software_cond"> |
11
f0ec41881020
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents:
10
diff
changeset
|
720 <param name="software" value="macs2" /> |
f0ec41881020
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents:
10
diff
changeset
|
721 <param name="input" value="macs_1.txt,macs_2.txt" /> |
f0ec41881020
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents:
10
diff
changeset
|
722 </conditional> |
f0ec41881020
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents:
10
diff
changeset
|
723 </repeat> |
f0ec41881020
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents:
10
diff
changeset
|
724 <repeat name="results"> |
f0ec41881020
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents:
10
diff
changeset
|
725 <conditional name="software_cond"> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
726 <param name="software" value="star" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
727 <repeat name="output"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
728 <conditional name="type"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
729 <param name="type" value="log"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
730 <param name="input" value="star_log.txt" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
731 </conditional> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
732 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
733 <repeat name="output"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
734 <conditional name="type"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
735 <param name="type" value="genecounts"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
736 <param name="input" value="star_counts.txt" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
737 </conditional> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
738 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
739 </conditional> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
740 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
741 <repeat name="results"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
742 <conditional name="software_cond"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
743 <param name="software" value="tophat" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
744 <param name="input" value="tophat.txt" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
745 </conditional> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
746 </repeat> |
18
c19b16e5729c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 263b1803fbf2622dbeb283b1d965690a5dc24ec9"
iuc
parents:
17
diff
changeset
|
747 <param name="saveLog" value="false"/> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
748 <output name="html_report"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
749 <assert_contents> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
750 <has_text text="bismark-alignment" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
751 <has_text text="bowtie2_se_plot" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
752 <has_text text="hisat2_se_plot" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
753 <has_text text="kallisto_alignment" /> |
11
f0ec41881020
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents:
10
diff
changeset
|
754 <has_text text="MACS2" /> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
755 <has_text text="star_alignment_plot" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
756 <has_text text="tophat_alignment" /> |
6
01237d721a9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361
iuc
parents:
5
diff
changeset
|
757 <has_text text="hicexplorer" /> |
9
df99138d2776
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 31d721c19f5681dfe542dd23185c06c8f29f1945
iuc
parents:
8
diff
changeset
|
758 <has_text text="hicexplorer1_log_1" /> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
759 </assert_contents> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
760 </output> |
20
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
761 <output_collection name="stats" type="list" count="11"> |
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
762 <expand macro="element_assert" name="bismark_alignment" columns="21" lines="2" text="bismark_txt_SE_report"/> |
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
763 <expand macro="element_assert" name="bowtie2" columns="7" lines="3" text="bowtie2_1_txt"/> |
22
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
764 <expand macro="element_assert" name="cutadapt" columns="9" lines="5" text="HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2"/> |
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
765 <expand macro="element_assert" name="general_stats" columns="22" lines="19" text="treat2"/> |
20
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
766 <expand macro="element_assert" name="hicexplorer" columns="41" lines="4" text="hicexplorer_3_hicexplorer2_log_small_test_rf"/> |
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
767 <expand macro="element_assert" name="hisat2" columns="6" lines="3" text="hisat2_2_txt"/> |
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
768 <expand macro="element_assert" name="kallisto" columns="6" lines="3" text="HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1"/> |
22
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
769 <expand macro="element_assert" name="macs" columns="12" lines="3" text="treat2"/> |
20
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
770 <expand macro="element_assert" name="sources" columns="4" lines="18" text="Cutadapt"/> |
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
771 <expand macro="element_assert" name="star" columns="27" lines="2" text="star_log_txt"/> |
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
772 <expand macro="element_assert" name="tophat.txt" columns="9" lines="2" text="tophat_txtalign"/> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
773 </output_collection> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
774 </test> |
22
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
775 <!--Test 03--> |
18
c19b16e5729c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 263b1803fbf2622dbeb283b1d965690a5dc24ec9"
iuc
parents:
17
diff
changeset
|
776 <test expect_num_outputs="2"> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
777 <repeat name="results"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
778 <conditional name="software_cond"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
779 <param name="software" value="bamtools" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
780 <param name="input" value="bamtools.txt" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
781 </conditional> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
782 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
783 <repeat name="results"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
784 <conditional name="software_cond"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
785 <param name="software" value="bcftools" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
786 <param name="input" value="bcftools.txt" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
787 </conditional> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
788 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
789 <repeat name="results"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
790 <conditional name="software_cond"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
791 <param name="software" value="busco" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
792 <param name="input" value="busco.txt" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
793 </conditional> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
794 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
795 <repeat name="results"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
796 <conditional name="software_cond"> |
8
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
797 <param name="software" value="deeptools" /> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
798 <repeat name="output"> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
799 <param name="type" value="bamPEFragmentSize"/> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
800 <param name="input" value="deeptools_bamPEFragmentSize.txt"/> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
801 </repeat> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
802 <repeat name="output"> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
803 <param name="type" value="estimateReadFiltering"/> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
804 <param name="input" value="deeptools_estimateReadFiltering.txt"/> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
805 </repeat> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
806 <repeat name="output"> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
807 <param name="type" value="plotCoverageStdout"/> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
808 <param name="input" value="deeptools_plotCoverageStdout.txt"/> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
809 </repeat> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
810 <repeat name="output"> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
811 <param name="type" value="plotCoverageOutRawCounts"/> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
812 <param name="input" value="deeptools_plotCoverageOutRawCounts.txt"/> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
813 </repeat> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
814 <repeat name="output"> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
815 <param name="type" value="plotEnrichment"/> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
816 <param name="input" value="deeptools_plotEnrichment.txt"/> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
817 </repeat> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
818 <repeat name="output"> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
819 <param name="type" value="plotFingerprintOutRawCounts"/> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
820 <param name="input" value="deeptools_plotFingerprintOutRawCounts.txt"/> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
821 </repeat> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
822 </conditional> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
823 </repeat> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
824 <repeat name="results"> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
825 <conditional name="software_cond"> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
826 <param name="software" value="featureCounts" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
827 <param name="input" value="featureCounts.txt" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
828 </conditional> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
829 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
830 <repeat name="results"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
831 <conditional name="software_cond"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
832 <param name="software" value="gatk" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
833 <repeat name="output"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
834 <param name="type" value="base_recalibrator"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
835 <param name="input" value="gatk_BaseRecalibrator.txt"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
836 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
837 <repeat name="output"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
838 <param name="type" value="varianteval"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
839 <param name="input" value="gatk_varianteval.txt"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
840 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
841 </conditional> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
842 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
843 <repeat name="results"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
844 <conditional name="software_cond"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
845 <param name="software" value="htseq" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
846 <param name="input" value="htseq.txt" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
847 </conditional> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
848 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
849 <repeat name="results"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
850 <conditional name="software_cond"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
851 <param name="software" value="picard" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
852 <repeat name="output"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
853 <param name="type" value="gcbias"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
854 <param name="input" value="picard_collectGcBias.txt"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
855 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
856 <repeat name="output"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
857 <param name="type" value="insertsize"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
858 <param name="input" value="picard_CollectInsertSizeMetrics.txt"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
859 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
860 <repeat name="output"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
861 <param name="type" value="markdups"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
862 <param name="input" value="picard_MarkDuplicates.txt"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
863 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
864 <repeat name="output"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
865 <param name="type" value="basedistributionbycycle"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
866 <param name="input" value="picard_CollectBaseDistributionByCycle.txt"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
867 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
868 <repeat name="output"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
869 <param name="type" value="rnaseqmetrics"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
870 <param name="input" value="picard_CollectRnaSeqMetrics.txt"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
871 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
872 <repeat name="output"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
873 <param name="type" value="alignment_metrics"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
874 <param name="input" value="picard_CollectAlignmentSummaryMetrics.txt"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
875 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
876 </conditional> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
877 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
878 <repeat name="results"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
879 <conditional name="software_cond"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
880 <param name="software" value="prokka" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
881 <param name="input" value="prokka_1.txt,prokka_2.txt" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
882 </conditional> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
883 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
884 <repeat name="results"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
885 <conditional name="software_cond"> |
16
bf675f34b056
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875"
iuc
parents:
15
diff
changeset
|
886 <param name="software" value="qualimap" /> |
bf675f34b056
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875"
iuc
parents:
15
diff
changeset
|
887 <param name="input" value="genome_results.txt" /> |
bf675f34b056
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875"
iuc
parents:
15
diff
changeset
|
888 </conditional> |
bf675f34b056
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875"
iuc
parents:
15
diff
changeset
|
889 </repeat> |
bf675f34b056
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875"
iuc
parents:
15
diff
changeset
|
890 <repeat name="results"> |
bf675f34b056
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875"
iuc
parents:
15
diff
changeset
|
891 <conditional name="software_cond"> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
892 <param name="software" value="quast" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
893 <param name="input" value="quast.tsv" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
894 </conditional> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
895 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
896 <repeat name="results"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
897 <conditional name="software_cond"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
898 <param name="software" value="rseqc" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
899 <repeat name="output"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
900 <conditional name="type"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
901 <param name="type" value="read_gc"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
902 <param name="input" value="rseqc.txt"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
903 </conditional> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
904 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
905 </conditional> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
906 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
907 <repeat name="results"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
908 <conditional name="software_cond"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
909 <param name="software" value="samblaster" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
910 <param name="input" value="samblaster.txt" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
911 </conditional> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
912 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
913 <repeat name="results"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
914 <conditional name="software_cond"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
915 <param name="software" value="samtools" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
916 <repeat name="output"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
917 <conditional name="type"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
918 <param name="type" value="stats"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
919 <param name="input" value="samtools_stats.txt"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
920 </conditional> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
921 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
922 <repeat name="output"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
923 <conditional name="type"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
924 <param name="type" value="flagstat"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
925 <param name="input" value="samtools_flagstat.txt"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
926 </conditional> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
927 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
928 <repeat name="output"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
929 <conditional name="type"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
930 <param name="type" value="idxstats"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
931 <param name="input" value="samtools_idxstats.txt"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
932 </conditional> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
933 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
934 </conditional> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
935 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
936 <repeat name="results"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
937 <conditional name="software_cond"> |
8
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
938 <param name="software" value="snpeff" /> |
22
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
939 <param name="input" value="snpeff.csv" ftype="csv" /> |
8
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
940 </conditional> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
941 </repeat> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
942 <repeat name="results"> |
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
943 <conditional name="software_cond"> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
944 <param name="software" value="vcftools" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
945 <repeat name="output"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
946 <conditional name="type"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
947 <param name="type" value="tstv_by_qual"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
948 <param name="input" value="vcftools.txt"/> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
949 </conditional> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
950 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
951 <param name="input" value="vcftools.txt" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
952 </conditional> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
953 </repeat> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
954 <output name="html_report"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
955 <assert_contents> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
956 <has_text text="bamtools-stats" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
957 <has_text text="bcftools_stats_indel-lengths" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
958 <has_text text="busco-lineage-fungi_odb9" /> |
8
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
959 <has_text text="deeptools" /> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
960 <has_text text="featureCounts_assignment_plot" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
961 <has_text text="gatk_varianteval_variant_plot" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
962 <has_text text="htseq_assignment_plot" /> |
22
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
963 <has_text text="picard_alignment_readlength" /> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
964 <has_text text="picard-rna-assignment" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
965 <has_text text="picard-markduplicates" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
966 <has_text text="picard-insertsize" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
967 <has_text text="picard-gcbias" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
968 <has_text text="prokka_plot" /> |
16
bf675f34b056
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875"
iuc
parents:
15
diff
changeset
|
969 <has_text text="qualimap" /> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
970 <has_text text="samblaster_duplicates" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
971 <has_text text="quast-stats" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
972 <has_text text="samtools-flagstat-dp" /> |
8
e0f4a651c6b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents:
7
diff
changeset
|
973 <has_text text="snpeff" /> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
974 </assert_contents> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
975 </output> |
20
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
976 <output_collection name="stats" type="list" count="21"> |
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
977 <expand macro="element_assert" name="bamtools_stats" columns="20" lines="2" text="bamtools_txt"/> |
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
978 <expand macro="element_assert" name="bcftools_stats" columns="28" lines="2" text="Test1"/> |
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
979 <expand macro="element_assert" name="busco" columns="8" lines="2" text="busco_txt"/> |
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
980 <expand macro="element_assert" name="featureCounts" columns="14" lines="7" text="5: TopHat on data 1, data 14, and data 13"/> |
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
981 <expand macro="element_assert" name="gatk_varianteval" columns="12" lines="2" text="gatk_varianteval_txt"/> |
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
982 <expand macro="element_assert" name="general_stats" columns="44" lines="23" text="x_bam"/> |
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
983 <expand macro="element_assert" name="htseq" columns="9" lines="2" text="htseq_txt"/> |
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
984 <expand macro="element_assert" name="picard_AlignmentSummaryMetrics" columns="26" lines="2" text="D11_H4K16ac_Rep1_R1_fastq_gz"/> |
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
985 <expand macro="element_assert" name="picard_RnaSeqMetrics" columns="27" lines="2" text="picard_CollectRnaSeqMetrics_bam"/> |
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
986 <expand macro="element_assert" name="picard_baseContent" columns="11" lines="2" text="D11_H4K16ac_Rep1_R1_fastq_gz"/> |
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
987 <expand macro="element_assert" name="picard_dups" columns="10" lines="2" text="dataset_114"/> |
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
988 <expand macro="element_assert" name="picard_insertSize" columns="23" lines="2" text="dataset_197_FR"/> |
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
989 <expand macro="element_assert" name="prokka" columns="11" lines="3" text="Sample2"/> |
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
990 <expand macro="element_assert" name="qualimap_bamqc_genome_results" columns="12" lines="2" text="x_bam"/> |
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
991 <expand macro="element_assert" name="quast" columns="50" lines="2" text="14892_1#15"/> |
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
992 <expand macro="element_assert" name="samblaster" columns="5" lines="2" text="virtual-normal"/> |
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
993 <expand macro="element_assert" name="samtools_flagstat" columns="34" lines="2" text="samtools_flagstat_txt"> |
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
994 <has_text text="samtools_flagstat" /> |
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
995 <has_text text="mapped_passed" /> |
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
996 <has_text text="20689039" /> |
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
997 </expand> |
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
998 <expand macro="element_assert" name="samtools_idxstats" columns="68" lines="2" text="samtools_idxstats_txt_idxstat"/> |
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
999 <expand macro="element_assert" name="samtools_stats" columns="40" lines="2" text="samtools_stats_txt"/> |
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
1000 <expand macro="element_assert" name="snpeff" columns="169" lines="2" text="snpeff_csv"/> |
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
1001 <expand macro="element_assert" name="sources" columns="4" lines="33" text="Bamtools"/> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
1002 </output_collection> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
1003 </test> |
22
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
1004 <!--Test 04--> |
18
c19b16e5729c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 263b1803fbf2622dbeb283b1d965690a5dc24ec9"
iuc
parents:
17
diff
changeset
|
1005 <test expect_num_outputs="2"> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
1006 <repeat name="results"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
1007 <conditional name="software_cond"> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
1008 <param name="software" value="custom_content" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
1009 <param name="cc_select" value="manual" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
1010 <param name="plot_type" value="linegraph" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
1011 <param name="section_name" value="BPC" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
1012 <param name="description" value="Sum of intensity (Y) of the most intense peaks at each retention time(X)" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
1013 <param name="xlab" value="Retention Time" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
1014 <param name="ylab" value="Base Peak Intensity" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
1015 <param name="input" value="cc_ko15.bpc.tab,cc_wt15.bpc.tab" /> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
1016 </conditional> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
1017 </repeat> |
22
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
1018 <output name="html_report" ftype="html"> |
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
1019 <assert_contents> |
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
1020 <has_size value="1110578" delta="500" /> |
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
1021 </assert_contents> |
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
1022 </output> |
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
1023 <output_collection name="stats" type="list" count="1"/> |
0
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff
changeset
|
1024 </test> |
22
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
1025 <!--Test 05--> |
18
c19b16e5729c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 263b1803fbf2622dbeb283b1d965690a5dc24ec9"
iuc
parents:
17
diff
changeset
|
1026 <test expect_num_outputs="3"> |
15
3d93dd18d9f8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6"
iuc
parents:
13
diff
changeset
|
1027 <repeat name="results"> |
3d93dd18d9f8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6"
iuc
parents:
13
diff
changeset
|
1028 <conditional name="software_cond"> |
3d93dd18d9f8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6"
iuc
parents:
13
diff
changeset
|
1029 <param name="software" value="fastqc" /> |
3d93dd18d9f8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6"
iuc
parents:
13
diff
changeset
|
1030 <repeat name="output"> |
3d93dd18d9f8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6"
iuc
parents:
13
diff
changeset
|
1031 <param name="type" value="data"/> |
3d93dd18d9f8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6"
iuc
parents:
13
diff
changeset
|
1032 <param name="input" value="fastqc_1.txt,fastqc_2.txt"/> |
3d93dd18d9f8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6"
iuc
parents:
13
diff
changeset
|
1033 </repeat> |
3d93dd18d9f8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6"
iuc
parents:
13
diff
changeset
|
1034 </conditional> |
3d93dd18d9f8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6"
iuc
parents:
13
diff
changeset
|
1035 </repeat> |
3d93dd18d9f8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6"
iuc
parents:
13
diff
changeset
|
1036 <param name="title" value="Title of the report"/> |
3d93dd18d9f8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6"
iuc
parents:
13
diff
changeset
|
1037 <param name="comment" value="Commment for the report"/> |
18
c19b16e5729c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 263b1803fbf2622dbeb283b1d965690a5dc24ec9"
iuc
parents:
17
diff
changeset
|
1038 <param name="flat" value="true"/> |
19
f7985e0479b9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 2b946616b7d12eed507d95ebbd8fd257ae37d83b"
iuc
parents:
18
diff
changeset
|
1039 <param name="export" value="true"/> |
15
3d93dd18d9f8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6"
iuc
parents:
13
diff
changeset
|
1040 <output name="html_report"> |
3d93dd18d9f8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6"
iuc
parents:
13
diff
changeset
|
1041 <assert_contents> |
3d93dd18d9f8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6"
iuc
parents:
13
diff
changeset
|
1042 <has_text text="Title of the report" /> |
3d93dd18d9f8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6"
iuc
parents:
13
diff
changeset
|
1043 <has_text text="Commment for the report" /> |
3d93dd18d9f8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6"
iuc
parents:
13
diff
changeset
|
1044 <has_text text="fastqc_seq_heatmap_key_t" /> |
3d93dd18d9f8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6"
iuc
parents:
13
diff
changeset
|
1045 </assert_contents> |
3d93dd18d9f8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6"
iuc
parents:
13
diff
changeset
|
1046 </output> |
20
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
1047 <output_collection name="stats" type="list" count="3"> |
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
1048 <expand macro="element_assert" name="fastqc" columns="22" lines="3" text="poulet5_2"/> |
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
1049 <expand macro="element_assert" name="general_stats" columns="6" lines="3" text="poulet5_2"/> |
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
1050 <expand macro="element_assert" name="sources" columns="4" lines="3" text="FastQC"/> |
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
1051 </output_collection> |
c1a4b5f3b432
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
iuc
parents:
19
diff
changeset
|
1052 <output_collection name="plots" type="list" count="7"> |
15
3d93dd18d9f8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6"
iuc
parents:
13
diff
changeset
|
1053 <element name="fastqc_per_base_sequence_quality_plot_1" file="mqc_fastqc_per_base_sequence_quality_plot_1.txt" compare="sim_size" delta="10"/> |
3d93dd18d9f8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6"
iuc
parents:
13
diff
changeset
|
1054 </output_collection> |
3d93dd18d9f8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6"
iuc
parents:
13
diff
changeset
|
1055 </test> |
22
9a913cdee30e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
21
diff
changeset
|
1056 <!--Test 06--> |
21
75c93c70d094
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
iuc
parents:
20
diff
changeset
|
1057 <test expect_num_outputs="2"> |
75c93c70d094
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
iuc
parents:
20
diff
changeset
|
1058 <repeat name="results"> |
75c93c70d094
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
iuc
parents:
20
diff
changeset
|
1059 <conditional name="software_cond"> |
75c93c70d094
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
iuc
parents:
20
diff
changeset
|
1060 <param name="software" value="pycoqc" /> |
75c93c70d094
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
iuc
parents:
20
diff
changeset
|
1061 <param name="input" value="pycoqc.json"/> |
75c93c70d094
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
iuc
parents:
20
diff
changeset
|
1062 </conditional> |
75c93c70d094
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
iuc
parents:
20
diff
changeset
|
1063 </repeat> |
75c93c70d094
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
iuc
parents:
20
diff
changeset
|
1064 <param name="title" value="Title of the report"/> |
75c93c70d094
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
iuc
parents:
20
diff
changeset
|
1065 <param name="comment" value="Commment for the report"/> |
75c93c70d094
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
iuc
parents:
20
diff
changeset
|
1066 <!-- <param name="flat" value="true"/> --> |
75c93c70d094
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
iuc
parents:
20
diff
changeset
|
1067 <output name="html_report"> |
75c93c70d094
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
iuc
parents:
20
diff
changeset
|
1068 <assert_contents> |
75c93c70d094
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
iuc
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|
1069 <has_text text="Title of the report" /> |
75c93c70d094
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
iuc
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diff
changeset
|
1070 <has_text text="Commment for the report" /> |
75c93c70d094
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
iuc
parents:
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diff
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|
1071 <has_text text="General Statistics" /> |
75c93c70d094
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
iuc
parents:
20
diff
changeset
|
1072 <has_text text="pycoqc_count_plot" /> |
75c93c70d094
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
iuc
parents:
20
diff
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|
1073 <has_text text="pycoqc_read_len_plot" /> |
75c93c70d094
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
iuc
parents:
20
diff
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|
1074 <has_text text="pycoqc_read_qual_plot" /> |
75c93c70d094
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
iuc
parents:
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diff
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|
1075 </assert_contents> |
75c93c70d094
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
iuc
parents:
20
diff
changeset
|
1076 </output> |
75c93c70d094
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
iuc
parents:
20
diff
changeset
|
1077 <output_collection name="stats" type="list" count="2"/> |
75c93c70d094
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
iuc
parents:
20
diff
changeset
|
1078 </test> |
23
abfd8a6544d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents:
22
diff
changeset
|
1079 <!--Test 07--> |
abfd8a6544d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents:
22
diff
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|
1080 <test expect_num_outputs="2"> |
abfd8a6544d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents:
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changeset
|
1081 <repeat name="results"> |
abfd8a6544d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents:
22
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changeset
|
1082 <conditional name="software_cond"> |
abfd8a6544d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents:
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diff
changeset
|
1083 <param name="software" value="rseqc" /> |
abfd8a6544d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents:
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|
1084 <repeat name="output"> |
abfd8a6544d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents:
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changeset
|
1085 <conditional name="type"> |
abfd8a6544d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents:
22
diff
changeset
|
1086 <param name="type" value="junction_annotation"/> |
abfd8a6544d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents:
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diff
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|
1087 <param name="input" value="junction_annotation.txt"/> |
abfd8a6544d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents:
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|
1088 </conditional> |
abfd8a6544d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents:
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|
1089 </repeat> |
abfd8a6544d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents:
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|
1090 <repeat name="output"> |
abfd8a6544d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents:
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|
1091 <conditional name="type"> |
abfd8a6544d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents:
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|
1092 <param name="type" value="junction_saturation"/> |
abfd8a6544d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents:
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|
1093 <param name="input" value="junction_saturation.txt"/> |
abfd8a6544d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents:
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1094 </conditional> |
abfd8a6544d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
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1095 </repeat> |
abfd8a6544d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents:
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1096 </conditional> |
abfd8a6544d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
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1097 </repeat> |
abfd8a6544d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents:
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|
1098 <param name="title" value="RSEQC report"/> |
abfd8a6544d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents:
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diff
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|
1099 <!-- <param name="flat" value="true"/> --> |
abfd8a6544d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
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|
1100 <output name="html_report"> |
abfd8a6544d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
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1101 <assert_contents> |
abfd8a6544d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents:
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|
1102 <has_text text="RSEQC report" /> |
abfd8a6544d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
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1103 <has_text text="Junction Annotation" /> |
abfd8a6544d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
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parents:
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1104 <has_text text="Junction Saturation" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
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1105 </assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
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1106 </output> |
abfd8a6544d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents:
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1107 <output_collection name="stats" type="list" count="2"/> |
abfd8a6544d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
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1108 </test> |
0
3bad335ccea9
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changeset
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1109 </tests> |
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|
1110 <help><![CDATA[ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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1111 **What it does** |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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|
1112 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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changeset
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1113 `MultiQC <http://multiqc.info/>`_ aggregates results from bioinformatics analyses across many samples into a single report. It takes results of multiple analyses and creates a report that can be viewed as a single beautiful web-page. It's a general use tool, perfect for summarizing the output from numerous bioinformatics tools. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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1114 |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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1115 **Inputs** |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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1116 |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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1117 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. 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 |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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1118 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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|
1119 ---- |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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1120 |
17
5e33b465d8d5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4eb6628314458d9426ea9e6fbf6e225d93e3d0fc"
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1121 The first integration of this tool was made by |
5e33b465d8d5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4eb6628314458d9426ea9e6fbf6e225d93e3d0fc"
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1122 `@cmonjeau <https://github.com/cmonjeau>`_ and `@yvanlebras <https://github.com/yvanlebras>`_. |
5e33b465d8d5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4eb6628314458d9426ea9e6fbf6e225d93e3d0fc"
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1123 It is now maintained by the `Intergalactic Utilities Commission <https://galaxyproject.org/iuc>`_. |
0
3bad335ccea9
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1124 ]]></help> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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|
1125 <citations> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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1126 <citation type="doi">10.1093/bioinformatics/btw354</citation> |
3bad335ccea9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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1127 </citations> |
3bad335ccea9
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1128 </tool> |