Mercurial > repos > bgruening > deeptools_correct_gc_bias
comparison correctGCBias.xml @ 17:3f84770b69cd draft
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
author | bgruening |
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date | Thu, 15 Feb 2018 07:44:32 -0500 |
parents | 297bccb7d5c6 |
children | 9e60bf557373 |
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16:f177dde2ae22 | 17:3f84770b69cd |
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1 <tool id="deeptools_correct_gc_bias" name="correctGCBias" version="@WRAPPER_VERSION@.0"> | 1 <tool id="deeptools_correct_gc_bias" name="correctGCBias" version="@WRAPPER_VERSION@.0"> |
2 <description>uses the output from computeGCBias to generate GC-corrected BAM files</description> | 2 <description>uses the output from computeGCBias to generate GC-corrected BAM/CRAM files</description> |
3 <macros> | 3 <macros> |
4 <token name="@BINARY@">correctGCBias</token> | 4 <token name="@BINARY@">correctGCBias</token> |
5 <import>deepTools_macros.xml</import> | 5 <import>deepTools_macros.xml</import> |
6 </macros> | 6 </macros> |
7 <expand macro="requirements" /> | 7 <expand macro="requirements" /> |
8 <command> | 8 <command> |
9 <![CDATA[ | 9 <![CDATA[ |
10 ln -s "$bamInput" "local_bamInput.bam" && | 10 ln -s "$bamInput" "local_bamInput.bam" && |
11 ln -s "$bamInput.metadata.bam_index" local_bamInput.bam.bai && | 11 #if $bamInput.ext == 'bam': |
12 ln -s '${bamInput.metadata.bam_index}' local_bamInput.bam.bai && | |
13 #else: | |
14 ln -s '${bamInput.metadata.cram_index}' local_bamInput.bam.crai && | |
15 #end if | |
12 | 16 |
13 @BINARY@ | 17 @BINARY@ |
14 @THREADS@ | 18 @THREADS@ |
15 --bamfile local_bamInput.bam | 19 --bamfile local_bamInput.bam |
16 --GCbiasFrequenciesFile "$GCbiasFrequenciesFile" | 20 --GCbiasFrequenciesFile "$GCbiasFrequenciesFile" |
29 --correctedFile corrected.bam | 33 --correctedFile corrected.bam |
30 ]]> | 34 ]]> |
31 </command> | 35 </command> |
32 <inputs> | 36 <inputs> |
33 <param argument="--GCbiasFrequenciesFile" type="data" format="tabular" label="Output of computeGCBias" help="" /> | 37 <param argument="--GCbiasFrequenciesFile" type="data" format="tabular" label="Output of computeGCBias" help="" /> |
34 <param argument="--bamInput" format="bam" type="data" | 38 <param argument="--bamInput" format="bam,cram" type="data" |
35 label="BAM file" help="This should be same file that was used for computeGCbias." /> | 39 label="BAM/CRAM file" help="This should be same file that was used for computeGCbias." /> |
36 <expand macro="reference_genome_source" /> | 40 <expand macro="reference_genome_source" /> |
37 <expand macro="effectiveGenomeSize" /> | 41 <expand macro="effectiveGenomeSize" /> |
38 <expand macro="region_limit_operation" /> | 42 <expand macro="region_limit_operation" /> |
39 </inputs> | 43 </inputs> |
40 <outputs> | 44 <outputs> |
46 <param name="bamInput" value="paired_chr2L.bam" ftype="bam" /> | 50 <param name="bamInput" value="paired_chr2L.bam" ftype="bam" /> |
47 <param name="ref_source" value="history" /> | 51 <param name="ref_source" value="history" /> |
48 <param name="input1" value="sequence.2bit" /> | 52 <param name="input1" value="sequence.2bit" /> |
49 <param name="effectiveGenomeSize_opt" value="specific" /> | 53 <param name="effectiveGenomeSize_opt" value="specific" /> |
50 <param name="effectiveGenomeSize" value="10050" /> | 54 <param name="effectiveGenomeSize" value="10050" /> |
51 <output name="outFileName" file="correctGCBias_result1.bam" ftype="bam" lines_diff="100" /> | 55 <output name="outFileName" file="correctGCBias_result1.bam" ftype="bam" lines_diff="200" /> |
52 </test> | 56 </test> |
53 </tests> | 57 </tests> |
54 <help> | 58 <help> |
55 <![CDATA[ | 59 <![CDATA[ |
56 | 60 |