| Previous changeset 6:30d427846764 (2018-01-02) Next changeset 8:707f691c974c (2018-03-07) |
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Commit message:
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01 |
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modified:
hicBuildMatrix.xml |
| b |
| diff -r 30d427846764 -r be42758f532e hicBuildMatrix.xml --- a/hicBuildMatrix.xml Tue Jan 02 10:14:52 2018 -0500 +++ b/hicBuildMatrix.xml Wed Jan 03 13:28:16 2018 -0500 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="hicexplorer_hicbuildmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.1"> +<tool id="hicexplorer_hicbuildmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.2"> <description>creates a contact matrix</description> <macros> <token name="@BINARY@">hicBuildMatrix</token> @@ -37,11 +37,8 @@ --region '$region' #end if - #if $outputFormat == 'h5' - --outFileName matrix.h5 - #elif $outputFormat == 'cool' - --outFileName matrix.cool - #end if + --outFileName matrix.$outputFormat + --outBam ./unsorted.bam $keepSelfCircles @@ -62,6 +59,7 @@ && mv $qc.files_path/hicQC.html $qc && mv $qc.files_path/*.log raw_qc + && mv matrix.$outputFormat matrix && samtools sort ./unsorted.bam -o sorted.bam ]]> @@ -122,14 +120,14 @@ </inputs> <outputs> <data name="outBam" from_work_dir="sorted.bam" format="bam" label="${tool.name} BAM file on ${on_string}"/> - <data name="outFileName_h5" from_work_dir="matrix.h5" format="h5" label="${tool.name} MATRIX on ${on_string}"> - <filter>outputFormat == 'h5'</filter> - </data> - <data name="outFileName_cool" from_work_dir="matrix.cool" format="cool" label="${tool.name} MATRIX on ${on_string}"> - <filter>outputFormat == 'cool'</filter> + <data name="outFileName" from_work_dir="matrix" format="h5" label="${tool.name} MATRIX on ${on_string}"> + <change_format> + <when input="outputFormat" value="cool" format="cool" /> + </change_format> </data> <data name="qc" format="html" label="${tool.name} QC"/> - <data name="raw_qc" from_work_dir='raw_qc' label="${tool.name} raw QC" /> + + <data name="raw_qc" from_work_dir='raw_qc' format='txt' label="${tool.name} raw QC" /> </outputs> <tests> <test> @@ -146,7 +144,7 @@ <param name='outputFormat' value='h5'/> <output name="outBam" file="small_test_matrix_result_sorted.bam" ftype="bam"/> - <output name="outFileName_h5" file="small_test_matrix_2.h5" ftype="h5" compare="sim_size"/> + <output name="outFileName" file="small_test_matrix_2.h5" ftype="h5" compare="sim_size"/> <output name="raw_qc" file='raw_qc_report' compare='diff' lines_diff='2'/> </test> </tests> @@ -212,7 +210,7 @@ Read orientation: _________________ - inward pairs -- outward pairs +- outward pairs - left pairs - right pairs |