Mercurial > repos > iuc > crossmap_bam
changeset 10:6ee334657360 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit ad4d739b4837dd61abc85614568d22f271f14568
| author | iuc |
|---|---|
| date | Mon, 02 Sep 2024 12:01:25 +0000 |
| parents | 158b5b2a164a |
| children | |
| files | crossmap_bam.xml macros.xml |
| diffstat | 2 files changed, 8 insertions(+), 16 deletions(-) [+] |
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--- a/crossmap_bam.xml Thu Jan 20 04:33:19 2022 +0000 +++ b/crossmap_bam.xml Mon Sep 02 12:01:25 2024 +0000 @@ -10,7 +10,7 @@ ln -s '${input}' ./input.bam && -CrossMap.py bam +CrossMap bam '${chain_source.input_chain}' $optional_tags @@ -23,33 +23,27 @@ ]]></command> <inputs> <param name="input" type="data" format="bam" label="BAM file"/> - - <expand macro="chain" /> - + <expand macro="chain"/> <param name="optional_tags" argument="-a" type="boolean" truevalue="-a" falsevalue="" label="Add optional BAM Headers"/> - <param name="insert_size" argument="-m" type="float" value="200.0" label="Insert size" help="Average insert size of pair-end sequencing (bp)"/> <param name="insert_size_stdev" argument="-s" type="float" value="30.0" label="Insert size std. dev" help="Stanadard deviation of insert size"/> - <param name="insert_size_fold" argument="-t" type="float" value="3.0" label="Insert size std. dev foldchange" - help="A mapped pair is considered as 'proper pair' if both ends mapped to different strand and the distance between them is less then '-t' * stdev from the mean"/> + <param name="insert_size_fold" argument="-t" type="float" value="3.0" label="Insert size std. dev foldchange" help="A mapped pair is considered as 'proper pair' if both ends mapped to different strand and the distance between them is less then '-t' * stdev from the mean"/> </inputs> - <outputs> - <data name="output" format="bam" label="${tool.name} on ${on_string}" from_work_dir="output.sorted.bam" /> + <data name="output" format="bam" label="${tool.name} on ${on_string}" from_work_dir="output.sorted.bam"/> <!-- CrossMap 0.2.5 does not produce output_unmapped --> </outputs> - <tests> <test> <param name="index_source" value="history"/> <param name="input" value="test_bam_01_input_a.bam" ftype="bam"/> <param name="input_chain" value="aToB.over.chain" ftype="csv"/> - <output name="output" file="test_bam_01_output_a.bam" ftype="bam" lines_diff="4" /> + <output name="output" file="test_bam_01_output_a.bam" ftype="bam" lines_diff="6"/> </test> <test> <param name="index_source" value="cached"/> <param name="input" value="test_bam_01_input_a.bam" ftype="bam" dbkey="hg18"/> - <output name="output" file="test_bam_01_output_a.bam" ftype="bam" lines_diff="4" /> + <output name="output" file="test_bam_01_output_a.bam" ftype="bam" lines_diff="6"/> </test> </tests> <help><![CDATA[ @@ -112,7 +106,6 @@ SU uniquely mapped ]]></help> - <citations> <citation type="doi">10.1093/bioinformatics/btt730</citation> </citations>
--- a/macros.xml Thu Jan 20 04:33:19 2022 +0000 +++ b/macros.xml Mon Sep 02 12:01:25 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">