Mercurial > repos > engineson > multiqc
annotate multiqc.xml @ 4:ff22ea7aa6bb draft
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
author | engineson |
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date | Fri, 27 May 2016 09:24:24 -0400 |
parents | 8f25feb85166 |
children | a9b6ec207609 |
rev | line source |
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0
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
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1 <tool id="multiqc" name="multiqc" version="0.6"> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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2 <description>aggregate results from bioinformatics analyses across many samples into a single report</description> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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changeset
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3 <requirements> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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4 <requirement type="package" version="0.6">multiqc</requirement> |
4
ff22ea7aa6bb
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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5 <requirement type="package" version="1.6.7">libpng</requirement> |
0
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
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6 </requirements> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
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7 <stdio> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
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8 <exit_code range="1:" /> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
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9 </stdio> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
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10 <command> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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changeset
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11 mkdir multiqc_WDir; |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
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12 |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
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13 #for $i, $repeat in enumerate( $results ) |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
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14 |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
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15 mkdir multiqc_WDir/${repeat.software}_${i}; |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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16 |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
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17 #if $repeat.software == "fastqc" |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
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18 |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
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19 #for $k, $file in enumerate ( $repeat.input_file ) |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
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20 ## create a directory for each file because of the unqiue name file parsing |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
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21 mkdir multiqc_WDir/${repeat.software}_${i}/file_${k}; |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
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22 ##cat ${file} > multiqc_WDir/${repeat.software}_${i}/file_$k/fastqc_data.txt; |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
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23 ln -s ${file} multiqc_WDir/${repeat.software}_${i}/file_$k/fastqc_data.txt; |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
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24 #end for |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
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25 |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
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26 #else if $repeat.software == "tophat" |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
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27 |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
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28 #for $file in $repeat.input_file |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
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29 ## test if input file name contains align_summary |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
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30 if [[ '${file.display_name}' =~ align_summary$ ]]; then |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
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31 ##cat ${file} > multiqc_WDir/${repeat.software}_${i}/'${file.display_name}'.txt; else |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
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32 ln -s ${file} multiqc_WDir/${repeat.software}_${i}/'${file.display_name}'.txt; else |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
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33 ##cat ${file} > multiqc_WDir/${repeat.software}_${i}/'${file.display_name}'_align_summary.txt; |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
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34 ln -s ${file} multiqc_WDir/${repeat.software}_${i}/'${file.display_name}'_align_summary.txt; |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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35 fi; |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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36 #end for |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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37 |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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changeset
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38 #else if $repeat.software == "cutadapt" |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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39 |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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changeset
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40 #for $file in $repeat.input_file |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
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41 cat ${file} > multiqc_WDir/${repeat.software}_${i}/'${file.display_name}'.txt; |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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42 ## replace header for old cutadapt release |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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43 sed -i 's/You are running/This is/' multiqc_WDir/${repeat.software}_${i}/'${file.display_name}'.txt; |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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44 #end for |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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45 |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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46 #else if $repeat.software == "featurecounts" |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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47 |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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48 #for $file in $repeat.input_file |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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49 ## remove spaces and colon to skip multiqc crash |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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changeset
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50 cat ${file} > multiqc_WDir/${repeat.software}_${i}/featurecounts_result.summary; |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
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51 ## remove spaces and colon to skip multiqc crash |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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52 sed -i 's/:/_/g' multiqc_WDir/${repeat.software}_${i}/featurecounts_result.summary; |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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53 sed -i 's/ /_/g' multiqc_WDir/${repeat.software}_${i}/featurecounts_result.summary; |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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54 #end for |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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55 |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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56 #else if $repeat.software == "bismark" |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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57 |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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58 #for $file in $repeat.input_file |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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59 ##cat ${file} > multiqc_WDir/${repeat.software}_${i}/'${file.display_name}'_SE_report.txt; |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
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60 ln -s ${file} multiqc_WDir/${repeat.software}_${i}/'${file.display_name}'_SE_report.txt; |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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61 #end for |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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62 |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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63 #else |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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64 |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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65 #for $file in $repeat.input_file |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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66 cat ${file} > multiqc_WDir/${repeat.software}_${i}/'${file.display_name}'; |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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67 #if $repeat.software == "picard" |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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68 sed -i 's/picard.sam.markduplicates.MarkDuplicates/picard.sam.MarkDuplicates/' multiqc_WDir/${repeat.software}_${i}/'${file.display_name}'; |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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69 #end if |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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70 #end for |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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71 |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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72 #end if |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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73 #end for |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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74 |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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75 multiqc multiqc_WDir; |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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76 |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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77 </command> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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78 <inputs> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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79 <!--param name="inputs" type="data" format="txt" multiple="true" label="Tools logs-outputs" /--> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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80 <repeat name="results" title="Results" min="1"> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
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81 <param name="software" type="select" label="Software name"> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
82 <option value="fastqc">FastQC (RawData file)</option> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
83 <option value="cutadapt">Cutadapt (Report file)</option> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
84 <option value="tophat">Tophat2 (align_summary file)</option> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
85 <option value="featurecounts">FeatureCounts (Summary file)</option> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
86 <option value="samtools_stats">Samtools Stats (Stats file)</option> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
87 <option value="picard">Picard (MarkDuplicates metrics file, CollectGTBiasMetrics Summary data file, CollectInsertSizeMetrics file)</option> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
88 <option value="bismark">Bismark (Report file)</option> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
89 <!--option value="bowtie2">Bowtie2</option> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
90 <option value="snpeff">SnpEff</option--> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
91 </param> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
92 <param name="input_file" type="data" format="txt, tabular" multiple="true" label="Result file" /> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
93 </repeat> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
94 </inputs> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
95 <outputs> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
96 <data format="html" from_work_dir="multiqc_report.html" name="html_file" label="${tool.name} on ${on_string}: Webpage" /> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
97 <data format="txt" name="text_file" from_work_dir="multiqc_data/.multiqc.log" label="${tool.name} on ${on_string}: Log"/> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
98 </outputs> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
99 <tests> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
100 <test> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
101 <repeat name="results"> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
102 <param name="software" value="fastqc" /> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
103 <param name="input_file" value="fastqc_data.txt" /> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
104 </repeat> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
105 <output name="html_file" file="report_fastqc.html" compare="sim_size" delta="1000"/> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
106 <output name="text_file" file="log_fastqc.txt" compare="sim_size" delta="1000"/> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
107 </test> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
108 <test> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
109 <repeat name="results"> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
110 <param name="software" value="fastqc" /> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
111 <param name="input_file" value="fastqc_data.txt,fastqc_data_2.txt" /> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
112 </repeat> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
113 <output name="html_file" file="report_fastqc_2.html" compare="sim_size" delta="1000"/> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
114 <output name="text_file" file="log_fastqc_2.txt" compare="sim_size" delta="1000"/> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
115 </test> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
116 <test> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
117 <repeat name="results"> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
118 <param name="software" value="cutadapt" /> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
119 <param name="input_file" value="cutadapt.txt" /> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
120 </repeat> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
121 <output name="html_file" file="report_cutadapt.html" compare="sim_size" delta="1000"/> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
122 <output name="text_file" file="log_cutadapt.txt" compare="sim_size" delta="1000"/> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
123 </test> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
124 <test> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
125 <repeat name="results"> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
126 <param name="software" value="tophat" /> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
127 <param name="input_file" value="tophat_data.txt" /> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
128 </repeat> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
129 <output name="html_file" file="report_tophat.html" compare="sim_size" delta="1000"/> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
130 <output name="text_file" file="log_tophat.txt" compare="sim_size" delta="1000"/> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
131 </test> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
132 <test> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
133 <repeat name="results"> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
134 <param name="software" value="featurecounts" /> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
135 <param name="input_file" value="featurecounts_data.txt" /> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
136 </repeat> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
137 <output name="html_file" file="report_featurecounts.html" compare="sim_size" delta="1000"/> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
138 <output name="text_file" file="log_featurecounts.txt" compare="sim_size" delta="1000"/> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
139 </test> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
140 <test> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
141 <repeat name="results"> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
142 <param name="software" value="picard" /> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
143 <param name="input_file" value="collectGcBias_data.txt,CollectInsertSizeMetrics.txt,MarkDuplicates_data.txt" /> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
144 </repeat> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
145 <output name="html_file" file="report_picard.html" compare="sim_size" delta="1000"/> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
146 <output name="text_file" file="log_picard.txt" compare="sim_size" delta="1000"/> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
147 </test> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
148 <test> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
149 <repeat name="results"> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
150 <param name="software" value="bismark" /> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
151 <param name="input_file" value="bismark_data.txt" /> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
152 </repeat> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
153 <output name="html_file" file="report_bismark.html" compare="sim_size" delta="1000"/> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
154 <output name="text_file" file="log_bismark.txt" compare="sim_size" delta="1000"/> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
155 </test> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
156 <test> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
157 <repeat name="results"> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
158 <param name="software" value="samtools_stats" /> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
159 <param name="input_file" value="samtools_data.txt" /> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
160 </repeat> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
161 <output name="html_file" file="report_samtools.html" compare="sim_size" delta="1000"/> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
162 <output name="text_file" file="log_samtools.txt" compare="sim_size" delta="1000"/> |
8f25feb85166
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 1110117e9b07da7913ea4480566a00d1bb373531-dirty
engineson
parents:
diff
changeset
|
163 </test> |
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164 <test> |
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165 <repeat name="results"> |
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166 <param name="software" value="fastqc" /> |
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167 <param name="input_file" value="fastqc_data.txt,fastqc_data_2.txt" /> |
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168 </repeat> |
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169 <repeat name="results"> |
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170 <param name="software" value="cutadapt" /> |
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171 <param name="input_file" value="cutadapt.txt" /> |
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172 </repeat> |
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173 <repeat name="results"> |
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174 <param name="software" value="tophat" /> |
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175 <param name="input_file" value="tophat_data.txt" /> |
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176 </repeat> |
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177 <repeat name="results"> |
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178 <param name="software" value="featurecounts" /> |
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179 <param name="input_file" value="featurecounts_data.txt" /> |
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180 </repeat> |
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181 <repeat name="results"> |
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182 <param name="software" value="picard" /> |
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183 <param name="input_file" value="collectGcBias_data.txt,CollectInsertSizeMetrics.txt,MarkDuplicates_data.txt" /> |
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184 </repeat> |
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185 <repeat name="results"> |
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186 <param name="software" value="bismark" /> |
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187 <param name="input_file" value="bismark_data.txt" /> |
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188 </repeat> |
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189 <repeat name="results"> |
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190 <param name="software" value="samtools_stats" /> |
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191 <param name="input_file" value="samtools_data.txt" /> |
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192 </repeat> |
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193 |
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194 <output name="html_file" file="report_all.html" compare="sim_size" delta="3000"/> |
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195 <output name="text_file" file="log_all.txt" compare="sim_size" delta="3000"/> |
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196 </test> |
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197 </tests> |
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198 |
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199 |
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200 <help> |
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201 **What it does** |
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202 |
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203 MultiQC aggregates results from bioinformatics analyses across many samples into a single report |
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204 |
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205 ---- |
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206 |
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207 **Description** |
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208 |
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209 MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. |
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210 |
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211 ---- |
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212 |
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213 **Inputs** |
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214 |
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215 MultiQC takes software outputs summary in order to create a single report. Below a list of compatible Galaxy tools : |
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216 |
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217 - Fastqc |
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218 - Cutadapt |
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219 - Tophat2 |
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220 - FeatureCounts |
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221 - Samtools stats |
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222 - Picard MarkDuplicates metrics |
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223 - Picard CollectGTBiasMetrics |
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224 - Picard CollectInsertSizeMetrics |
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225 - Bismark |
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226 |
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227 ---- |
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228 |
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229 **Integrated by:** |
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230 |
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231 Cyril Monjeaud and Yvan Le Bras |
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232 |
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233 `EnginesOn <http://engineson.fr/>`_ and Rennes GenOuest Bio-informatics Core Facility |
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234 |
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235 </help> |
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236 |
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237 <citations> |
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238 <citation type="bibtex">@proceedings{proceedings, |
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239 author = {Phil Ewels, Måns Magnusson, Max Käller}, |
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240 title = {Quality control at scale: MultiQC - Intelligent analysis reporting}, |
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241 journal = {Epigenomics of Common Disease}, |
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242 year = {2015}, |
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243 } |
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244 </citation> |
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245 </citations> |
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246 </tool> |
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247 |