Mercurial > repos > devteam > bam_to_sam
diff bam_to_sam.xml @ 5:f57df915aa10 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
author | iuc |
---|---|
date | Tue, 09 May 2017 11:18:39 -0400 |
parents | af7c50162f0b |
children | 10184eaa85fc |
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--- 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 @@ -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>