| Previous changeset 1:0c13bd882a1a (2018-01-02) Next changeset 3:303558d3bc11 (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:
hicTransform.xml |
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| diff -r 0c13bd882a1a -r 3106dcd651f5 hicTransform.xml --- a/hicTransform.xml Tue Jan 02 10:17:50 2018 -0500 +++ b/hicTransform.xml Wed Jan 03 13:31:00 2018 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="hicexplorer_hictransform" name="@BINARY@" version="@WRAPPER_VERSION@.0"> +<tool id="hicexplorer_hictransform" name="@BINARY@" version="@WRAPPER_VERSION@.1"> <description>transforms a matrix to a obs_exp, pearson and covariance matrix</description> <macros> <token name="@BINARY@">hicTransform</token> @@ -10,13 +10,10 @@ hicTransform --matrix '$matrix_h5_cooler' --method all - - #if $outputFormat == 'h5' - --outFileName matrix.h5 - #elif $outputFormat == 'cool' - --outFileName matrix.cool - #end if - + --outFileName matrix.$outputFormat + && mv obs_exp_matrix.$outputFormat obs_exp_matrix + && mv pearson_matrix.$outputFormat pearson_matrix + && mv covariance_matrix.$outputFormat covariance_matrix ]]> </command> <inputs> @@ -28,23 +25,20 @@ </inputs> <outputs> - <data name="obs_exp_h5" from_work_dir="obs_exp_matrix.h5" format="h5"> - <filter>outputFormat == 'h5'</filter> - </data> - <data name="pearson_h5" from_work_dir="pearson_matrix.h5" format="h5"> - <filter>outputFormat == 'h5'</filter> - </data> - <data name="covariance_h5" from_work_dir="covariance_matrix.h5" format="h5"> - <filter>outputFormat == 'h5'</filter> + <data name="obs_exp" from_work_dir="obs_exp_matrix" format="h5"> + <change_format> + <when input="outputFormat" value="cool" format="cool" /> + </change_format> </data> - <data name="obs_exp_cool" from_work_dir="obs_exp_matrix.cool" format="cool"> - <filter>outputFormat == 'cool'</filter> + <data name="pearson" from_work_dir="pearson_matrix" format="h5"> + <change_format> + <when input="outputFormat" value="cool" format="cool" /> + </change_format> </data> - <data name="pearson_cool" from_work_dir="pearson_matrix.cool" format="cool"> - <filter>outputFormat == 'cool'</filter> - </data> - <data name="covariance_cool" from_work_dir="covariance_matrix.cool" format="cool"> - <filter>outputFormat == 'cool'</filter> + <data name="covariance" from_work_dir="covariance_matrix" format="h5"> + <change_format> + <when input="outputFormat" value="cool" format="cool" /> + </change_format> </data> </outputs> @@ -52,16 +46,16 @@ <test> <param name="matrix_h5_cooler" value="small_test_matrix_50kb_res.h5"/> <param name="outputFormat" value="h5" /> - <output name="obs_exp_h5" file="obs_exp_small_50kb.h5" ftype="h5" compare="sim_size"/> - <output name="pearson_h5" file="pearson_small_50kb.h5" ftype="h5" compare="sim_size"/> - <output name="covariance_h5" file="covariance_small_50kb.h5" ftype="h5" compare="sim_size"/> + <output name="obs_exp" file="obs_exp_small_50kb.h5" ftype="h5" compare="sim_size"/> + <output name="pearson" file="pearson_small_50kb.h5" ftype="h5" compare="sim_size"/> + <output name="covariance" file="covariance_small_50kb.h5" ftype="h5" compare="sim_size"/> </test> <test> <param name="matrix_h5_cooler" value="small_test_matrix_50kb_res.h5"/> <param name="outputFormat" value="cool" /> - <output name="obs_exp_cool" file="obs_exp_small_50kb.cool" ftype="cool" compare="sim_size"/> - <output name="pearson_cool" file="pearson_small_50kb.cool" ftype="cool" compare="sim_size"/> - <output name="covariance_cool" file="covariance_small_50kb.cool" ftype="cool" compare="sim_size"/> + <output name="obs_exp" file="obs_exp_small_50kb.cool" ftype="cool" compare="sim_size"/> + <output name="pearson" file="pearson_small_50kb.cool" ftype="cool" compare="sim_size"/> + <output name="covariance" file="covariance_small_50kb.cool" ftype="cool" compare="sim_size"/> </test> </tests> <help><![CDATA[ |