| Previous changeset 8:e72c320c17c1 (2022-01-20) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit ad4d739b4837dd61abc85614568d22f271f14568 |
|
modified:
crossmap_wig.xml macros.xml |
| b |
| diff -r e72c320c17c1 -r f7229c8445da crossmap_wig.xml --- a/crossmap_wig.xml Thu Jan 20 04:30:30 2022 +0000 +++ b/crossmap_wig.xml Mon Sep 02 12:01:52 2024 +0000 |
| [ |
| @@ -7,38 +7,32 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ -CrossMap.py wig +CrossMap wig '${chain_source.input_chain}' '${input}' output ]]></command> - <inputs> <param name="input" type="data" format="wig" label="Wiggle file"/> - - <expand macro="chain" /> + <expand macro="chain"/> </inputs> - <outputs> - <data name="output" format="bigwig" label="${tool.name} on ${on_string}" from_work_dir="output.bw" /> - <data name="output2" format="bedgraph" label="${tool.name} (bedgraph) on ${on_string}" from_work_dir="output.sorted.bgr" /> + <data name="output" format="bigwig" label="${tool.name} on ${on_string}" from_work_dir="output.bw"/> + <data name="output2" format="bedgraph" label="${tool.name} (bedgraph) on ${on_string}" from_work_dir="output.sorted.bgr"/> </outputs> - <tests> - <!-- WIG - Doesn't understand fixedStep --> + <!-- WIG - Doesn't understand fixedStep --> <test> <param name="input" value="test_wig_01_input_a.wig" ftype="wig"/> <param name="index_source" value="history"/> <param name="input_chain" value="aToB.over.chain" ftype="csv"/> - <output name="output" file="test_wig_01_output_a.bw"/> <output name="output2" file="test_wig_01_output_a.sorted.bgr"/> </test> - - <test><!-- cached reference genome --> - <param name="input" value="test_wig_01_input_a.wig" ftype="wig" dbkey="hg18" /> + <test> + <!-- cached reference genome --> + <param name="input" value="test_wig_01_input_a.wig" ftype="wig" dbkey="hg18"/> <param name="index_source" value="cached"/> - <output name="output" file="test_wig_01_output_a.bw"/> <output name="output2" file="test_wig_01_output_a.sorted.bgr"/> </test> @@ -57,7 +51,6 @@ smaller than file in wiggle format, and more importantly, CrossMap internally transforms wiggle into bedGraph to increase running speed. ]]></help> - <citations> <citation type="doi">10.1093/bioinformatics/btt730</citation> </citations> |
| b |
| diff -r e72c320c17c1 -r f7229c8445da macros.xml --- a/macros.xml Thu Jan 20 04:30:30 2022 +0000 +++ b/macros.xml Mon Sep 02 12:01:52 2024 +0000 |
| [ |
| @@ -1,4 +1,3 @@ -<?xml version="1.0"?> <macros> <xml name="requirements"> <requirements> @@ -6,7 +5,7 @@ <yield/> </requirements> </xml> - <token name="@TOOL_VERSION@">0.6.1</token> + <token name="@TOOL_VERSION@">0.7.0</token> <token name="@VERSION_SUFFIX@">0</token> <xml name="stdio"> <stdio> @@ -17,7 +16,7 @@ </xml> <xml name="version_command"> <version_command><![CDATA[ -CrossMap.py 2>&1 | head -n 1 | grep -E --only-matching 'CrossMap.*' +CrossMap 2>&1 | head -n 1 | grep -E --only-matching 'CrossMap.*' ]]></version_command> </xml> <xml name="chain"> |