| Previous changeset 0:020e144b5f78 (2015-04-21) Next changeset 2:30388d878f81 (2020-07-02) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 |
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modified:
macros.xml samtools_reheader.xml |
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removed:
tool_dependencies.xml |
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| diff -r 020e144b5f78 -r db000c6007a0 macros.xml --- a/macros.xml Tue Apr 21 16:57:10 2015 -0400 +++ b/macros.xml Tue May 09 11:18:23 2017 -0400 |
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| @@ -1,16 +1,17 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="1.2">samtools</requirement> + <requirement type="package" version="1.3.1">samtools</requirement> <yield/> </requirements> </xml> + <token name="@TOOL_VERSION@">1.3.1</token> <xml name="citations"> <citations> <citation type="bibtex"> @misc{SAM_def, title={Definition of SAM/BAM format}, - url = {https://samtools.github.io/hts-specs/SAMv1.pdf},} + url = {https://samtools.github.io/hts-specs/},} </citation> <citation type="doi">10.1093/bioinformatics/btp352</citation> <citation type="doi">10.1093/bioinformatics/btr076</citation> @@ -41,7 +42,7 @@ </citations> </xml> <xml name="version_command"> - <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command> + <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command> </xml> <xml name="stdio"> <stdio> @@ -64,7 +65,5 @@ 5. Click **Save** The medatada will be re-detected and you will be able to see the list of reference sequences in the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop-down. - </token> - </macros> |
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| diff -r 020e144b5f78 -r db000c6007a0 samtools_reheader.xml --- a/samtools_reheader.xml Tue Apr 21 16:57:10 2015 -0400 +++ b/samtools_reheader.xml Tue May 09 11:18:23 2017 -0400 |
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| @@ -1,12 +1,17 @@ -<tool id="samtools_reheader" name="Reheader" version="2.0"> +<tool id="samtools_reheader" name="Reheader" version="2.0.1"> <description>copy SAM/BAM header between datasets</description> <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements"></expand> - <expand macro="stdio"></expand> - <expand macro="version_command"></expand> - <command><![CDATA[samtools reheader "${input_header}" "${input_file}" > "${output}"]]></command> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <expand macro="version_command"/> + <command><![CDATA[ + samtools reheader + '${input_header}' + '${input_file}' + > '${output}' + ]]></command> <inputs> <param name="input_header" type="data" format="sam,bam" label="Select source dataset" help="Header from this dataset will be used to replace header in the target dataset. May be either SAM or BAM dataset."/> <param name="input_file" type="data" format="bam" label="Select target dataset" help="Header from the source dataset will be inserted here. Should be a BAM dataset."/> @@ -18,15 +23,14 @@ <test> <param name="input_header" ftype="bam" value="reheader_input_header.bam"/> <param name="input_file" ftype="bam" value="reheader_input_file.bam"/> - <output name="output" ftype="bam" file="reheader_out.bam"/> + <output name="output" ftype="bam" file="reheader_out.bam" lines_diff="1"/><!-- samtools adds reheader line --> </test> </tests> <help> **What it does** Copies header from *source* dataset into *target* dataset using ``samtools reheader`` command. - </help> - <expand macro="citations"></expand> + <expand macro="citations"/> </tool> |
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| diff -r 020e144b5f78 -r db000c6007a0 tool_dependencies.xml --- a/tool_dependencies.xml Tue Apr 21 16:57:10 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="samtools" version="1.2"> - <repository changeset_revision="6eea04363026" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |