| Previous changeset 4:af7c50162f0b (2015-04-21) Next changeset 6:88eedb4abea0 (2018-10-14) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 |
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modified:
bam_to_sam.xml macros.xml |
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removed:
tool_dependencies.xml |
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| diff -r af7c50162f0b -r f57df915aa10 bam_to_sam.xml --- a/bam_to_sam.xml Tue Apr 21 14:36:15 2015 -0400 +++ b/bam_to_sam.xml Tue May 09 11:18:39 2017 -0400 |
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| @@ -1,21 +1,23 @@ -<tool id="bam_to_sam" name="BAM-to-SAM" version="2.0"> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements"></expand> - <expand macro="version_command"></expand> - <expand macro="stdio"></expand> - <description>convert BAM to SAM</description> - <command> -<![CDATA[ - samtools view -o "${output1}" ${header} "${input1}" -]]> - </command> +<tool id="bam_to_sam" name="BAM-to-SAM" version="2.0.1"> + <description>convert BAM to SAM</description> + + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <expand macro="version_command"/> + + <command><![CDATA[ + samtools view -o '${output1}' ${header} '${input1}' + ]]></command> + <inputs> - <param format="bam" label="BAM File to Convert" name="input1" type="data" /> - <param name="header" label="Header options" type="select" help="Allows to choose between seeing the entire dataset with the header, header only, or data only."> + <param format="bam" name="input1" type="data" label="BAM File to Convert" /> + <param name="header" label="Header options" type="select" + help="Allows to choose between seeing the entire dataset with the header, header only, or data only."> <option value="-h">Include header in SAM output (-h)</option> - <option value="-H">Print header only (-H)</option> + <option value="-H">Return header only (-H)</option> <option value="">Exclude header</option> </param> </inputs> @@ -26,29 +28,23 @@ <test> <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" /> <param name="header" value="-h" /> - <output file="bam_to_sam_out1.sam" name="output1" sorted="True" /> + <output file="bam_to_sam_out1.sam" name="output1" /> </test> <test> <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" /> <param name="header" value="-H" /> - <output file="bam_to_sam_out2.sam" name="output1" sorted="True" /> + <output file="bam_to_sam_out2.sam" name="output1" /> </test> <test> <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" /> <param name="header" value="" /> - <output file="bam_to_sam_out3.sam" name="output1" sorted="True" /> + <output file="bam_to_sam_out3.sam" name="output1" /> </test> </tests> - <help> -<![CDATA[ - + <help><![CDATA[ **What it does** -Converts BAM dataset to SAM using ``samtools view`` command:: - - samtools view -o [OUTPUT SAM] [-h|-H] [INPUT BAM] - -]]> - </help> - <expand macro="citations"></expand> +Converts BAM dataset to SAM using the ``samtools view`` command. + ]]></help> + <expand macro="citations"/> </tool> |
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| diff -r af7c50162f0b -r f57df915aa10 macros.xml --- a/macros.xml Tue Apr 21 14:36:15 2015 -0400 +++ b/macros.xml Tue May 09 11:18:39 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 af7c50162f0b -r f57df915aa10 tool_dependencies.xml --- a/tool_dependencies.xml Tue Apr 21 14:36:15 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> |