| Previous changeset 2:083774cc8472 (2017-10-20) Next changeset 4:5051467dc96a (2019-09-11) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 23fab16cd40acbd5b0e9d640ed3858040db7a622 |
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modified:
crossmap_bam.xml macros.xml |
| b |
| diff -r 083774cc8472 -r cb3557cabc7b crossmap_bam.xml --- a/crossmap_bam.xml Fri Oct 20 11:33:02 2017 -0400 +++ b/crossmap_bam.xml Thu May 24 19:10:46 2018 -0400 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="crossmap_bam" name="CrossMap BAM" version="@WRAPPER_VERSION@-0"> +<tool id="crossmap_bam" name="CrossMap BAM" version="@WRAPPER_VERSION@"> <description>Convert genome coordinates or annotation files between genome assemblies</description> <macros> <import>macros.xml</import> @@ -7,7 +7,6 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - CrossMap.py bam '${chain_source.input_chain}' $optional_tags @@ -17,9 +16,7 @@ -t $insert_size_fold '${input}' -'${output}' - -&& mv '${output}.sorted.bam' '${output}' +output ]]></command> <inputs> <param name="input" type="data" format="bam" label="BAM file"/> @@ -34,7 +31,7 @@ </inputs> <outputs> - <data name="output" format="bam" label="${tool.name} on ${on_string}" /> + <data name="output" format="bam" label="${tool.name} on ${on_string}" from_work_dir="output.sorted.bam" /> <!-- CrossMap 0.2.5 does not produce output_unmapped --> </outputs> @@ -45,7 +42,7 @@ <param name="input_chain" value="aToB.over.chain" ftype="csv"/> <param name="include_fails" value="False"/> - <output name="output" file="test_bam_01_output_a.bam" compare="diff" lines_diff="8"/> + <output name="output" file="test_bam_01_output_a.bam" ftype="bam" /> </test> <test> <param name="index_source" value="cached"/> @@ -53,7 +50,7 @@ <param name="input" value="test_bam_01_input_a.bam" ftype="bam" dbkey="hg18"/> <param name="include_fails" value="False"/> - <output name="output" file="test_bam_01_output_a.bam" compare="diff" lines_diff="8"/> + <output name="output" file="test_bam_01_output_a.bam" ftype="bam" /> </test> </tests> <help><![CDATA[ @@ -115,7 +112,6 @@ multiple mapped SU uniquely mapped - ]]></help> <citations> |
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| diff -r 083774cc8472 -r cb3557cabc7b macros.xml --- a/macros.xml Fri Oct 20 11:33:02 2017 -0400 +++ b/macros.xml Thu May 24 19:10:46 2018 -0400 |
| b |
| @@ -2,11 +2,11 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="0.2.5">crossmap</requirement> + <requirement type="package" version="0.2.7">crossmap</requirement> <yield/> </requirements> </xml> - <token name="@WRAPPER_VERSION@">0.2.5</token> + <token name="@WRAPPER_VERSION@">0.2.7</token> <xml name="stdio"> <stdio> <regex match="Aborted (core dumped)" source="stdout" level="fatal"/> |