Mercurial > repos > bgruening > deeptools_compute_gc_bias
comparison computeGCBias.xml @ 17:1795fdfc23b8 draft
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
| author | bgruening |
|---|---|
| date | Thu, 15 Feb 2018 07:54:32 -0500 |
| parents | 4c03a58a512e |
| children | f0fd1cdbe506 |
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| 16:e6a06ce6ac46 | 17:1795fdfc23b8 |
|---|---|
| 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 $outFileName | 20 --GCbiasFrequenciesFile $outFileName |
| 17 --fragmentLength $fragmentLength | 21 |
| 22 #if $fragmentLength != "": | |
| 23 --fragmentLength $fragmentLength | |
| 24 #end if | |
| 18 | 25 |
| 19 @reference_genome_source@ | 26 @reference_genome_source@ |
| 20 | 27 |
| 21 #if $effectiveGenomeSize.effectiveGenomeSize_opt == "specific": | 28 #if $effectiveGenomeSize.effectiveGenomeSize_opt == "specific": |
| 22 --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize | 29 --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize |
| 44 --plotFileFormat $image_format | 51 --plotFileFormat $image_format |
| 45 #end if | 52 #end if |
| 46 ]]> | 53 ]]> |
| 47 </command> | 54 </command> |
| 48 <inputs> | 55 <inputs> |
| 49 <param name="bamInput" format="bam" type="data" label="BAM file" | 56 <param name="bamInput" format="bam,cram" type="data" label="BAM file" |
| 50 help=""/> | 57 help=""/> |
| 51 | 58 |
| 52 <expand macro="reference_genome_source" /> | 59 <expand macro="reference_genome_source" /> |
| 53 <expand macro="effectiveGenomeSize" /> | 60 <expand macro="effectiveGenomeSize" /> |
| 54 <expand macro="fragmentLength" /> | 61 <expand macro="fragmentLength" /> |
| 82 <option value="none">No image</option> | 89 <option value="none">No image</option> |
| 83 <option value="png" selected="true">Image in png format</option> | 90 <option value="png" selected="true">Image in png format</option> |
| 84 <option value="pdf">Image in pdf format</option> | 91 <option value="pdf">Image in pdf format</option> |
| 85 <option value="svg">Image in svg format</option> | 92 <option value="svg">Image in svg format</option> |
| 86 <option value="eps">Image in eps format</option> | 93 <option value="eps">Image in eps format</option> |
| 94 <option value="plotly">HTML page rendered with plotly</option> | |
| 87 </param> | 95 </param> |
| 88 </inputs> | 96 </inputs> |
| 89 <outputs> | 97 <outputs> |
| 90 <data name="outFileName" format="tabular" /> | 98 <data name="outFileName" format="tabular" /> |
| 91 <data name="outImageName" format="png" label="${tool.name} GC-bias Plot"> | 99 <data name="outImageName" format="png" label="${tool.name} GC-bias Plot"> |
| 96 </filter> | 104 </filter> |
| 97 <change_format> | 105 <change_format> |
| 98 <when input="image_format" value="pdf" format="pdf" /> | 106 <when input="image_format" value="pdf" format="pdf" /> |
| 99 <when input="image_format" value="svg" format="svg" /> | 107 <when input="image_format" value="svg" format="svg" /> |
| 100 <when input="image_format" value="eps" format="eps" /> | 108 <when input="image_format" value="eps" format="eps" /> |
| 109 <when input="image_format" value="plotly" format="html" /> | |
| 101 </change_format> | 110 </change_format> |
| 102 </data> | 111 </data> |
| 103 </outputs> | 112 </outputs> |
| 104 <tests> | 113 <tests> |
| 105 <test> | 114 <test> |
| 112 <param name="sampleSize" value="10" /> | 121 <param name="sampleSize" value="10" /> |
| 113 <param name="effectiveGenomeSize_opt" value="specific" /> | 122 <param name="effectiveGenomeSize_opt" value="specific" /> |
| 114 <param name="effectiveGenomeSize" value="10050" /> | 123 <param name="effectiveGenomeSize" value="10050" /> |
| 115 <param name="region" value="chr2L" /> | 124 <param name="region" value="chr2L" /> |
| 116 <param name="image_format" value="none" /> | 125 <param name="image_format" value="none" /> |
| 126 <param name="fragmentLength" value="300" /> | |
| 117 <output name="outFileName" file="computeGCBias_result1.tabular" ftype="tabular" /> | 127 <output name="outFileName" file="computeGCBias_result1.tabular" ftype="tabular" /> |
| 118 </test> | 128 </test> |
| 119 </tests> | 129 </tests> |
| 120 <help> | 130 <help> |
| 121 <![CDATA[ | 131 <![CDATA[ |