| Previous changeset 1:d5a86de86846 (2018-01-02) Next changeset 3:ea50f7bba657 (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:
hicPCA.xml |
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| diff -r d5a86de86846 -r 97c797606746 hicPCA.xml --- a/hicPCA.xml Tue Jan 02 10:19:28 2018 -0500 +++ b/hicPCA.xml Wed Jan 03 13:32:31 2018 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="hicexplorer_hicpca" name="@BINARY@" version="@WRAPPER_VERSION@.0"> +<tool id="hicexplorer_hicpca" name="@BINARY@" version="@WRAPPER_VERSION@.1"> <description>computes the principal components for A / B compartment analysis</description> <macros> <token name="@BINARY@">hicPCA</token> @@ -9,54 +9,51 @@ hicPCA --matrix '$matrix_h5_cooler' - #if $outputFormat == 'bigwig' - --outputFileName 'pca1.bigwig' 'pca2.bigwig' - --format bigwig - #elif $outputFormat == 'bedgraph' - --outputFileName 'pca1.bedgraph' 'pca2.bedgraph' - --format bedgraph - #end if + --outputFileName pca1.$outputFormat pca2.$outputFormat + --format $outputFormat + + && mv pca1.$outputFormat pca1 + && mv pca2.$outputFormat pca2 ]]> </command> <inputs> <expand macro='matrix_h5_cooler_macro' /> <param name='outputFormat' type='select' label="Output file format"> - <option value='bigwig'>bigwig</option> + <option value='bigwig' selected="true">bigwig</option> <option value="bedgraph">bedgraph</option> </param> </inputs> <outputs> - <data name="pca1_bw" from_work_dir="pca1.bigwig" format="bigwig"> + <data name="pca1" from_work_dir="pca1" format="bigwig"> <filter>outputFormat == 'bigwig'</filter> + <change_format> + <when input="outputFormat" value="bedgraph" format="bedgraph" /> + </change_format> </data> - <data name="pca2_bw" from_work_dir="pca2.bigwig" format="bigwig"> - <filter>outputFormat == 'bigwig'</filter> + <data name="pca2" from_work_dir="pca2" format="bigwig"> + <change_format> + <when input="outputFormat" value="bedgraph" format="bedgraph" /> + </change_format> </data> - <data name="pca1_bedgraph" from_work_dir="pca1.bedgraph" format="bedgraph"> - <filter>outputFormat == 'bedgraph'</filter> - </data> - <data name="pca2_bedgraph" from_work_dir="pca2.bedgraph" format="bedgraph"> - <filter>outputFormat == 'bedgraph'</filter> - </data> </outputs> <tests> <test> <param name="matrix_h5_cooler" value="small_test_matrix_50kb_res.h5"/> <param name="outputFormat" value="bedgraph" /> - <output name="pca1_bedgraph" file="pca1.bedgraph" ftype="bedgraph" compare="sim_size"/> - <output name="pca2_bedgraph" file="pca2.bedgraph" ftype="bedgraph" compare="sim_size"/> + <output name="pca1" file="pca1.bedgraph" ftype="bedgraph" compare="sim_size"/> + <output name="pca2" file="pca2.bedgraph" ftype="bedgraph" compare="sim_size"/> </test> <test> <param name="matrix_h5_cooler" value="small_test_matrix_50kb_res.h5"/> <param name="outputFormat" value="bigwig" /> - <output name="pca1_bw" file="pca1.bw" ftype="bigwig" compare="sim_size"/> - <output name="pca2_bw" file="pca2.bw" ftype="bigwig" compare="sim_size"/> + <output name="pca1" file="pca1.bw" ftype="bigwig" compare="sim_size"/> + <output name="pca2" file="pca2.bw" ftype="bigwig" compare="sim_size"/> </test> </tests> <help><![CDATA[ |