Mercurial > repos > devteam > samtools_slice_bam
diff samtools_slice_bam.xml @ 4:344fc91e1bfd draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
| author | iuc |
|---|---|
| date | Tue, 28 Sep 2021 16:16:30 +0000 |
| parents | a4a10c7924d1 |
| children | b5c88b7b153e |
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--- a/samtools_slice_bam.xml Tue May 09 11:17:27 2017 -0400 +++ b/samtools_slice_bam.xml Tue Sep 28 16:16:30 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="samtools_slice_bam" name="Slice" version="2.0.1"> +<tool id="samtools_slice_bam" name="Slice" version="2.0.2" profile="@PROFILE@"> <description>BAM by genomic regions</description> <macros> <import>macros.xml</import> @@ -13,12 +13,12 @@ ln -s '${input_bam.metadata.bam_index}' temp_input.bam.bai && #if str($slice_method.slice_method_selector) == "bed": - samtools view -@ \${GALAXY_SLOTS:-1} -b -L "${input_interval}" -o unsorted_output.bam temp_input.bam && + samtools view -@ \${GALAXY_SLOTS:-1} -b -L "${input_interval}" -o unsorted_output.bam temp_input.bam && #elif str($slice_method.slice_method_selector) == "chr": - samtools view -@ \${GALAXY_SLOTS:-1} -b -o unsorted_output.bam temp_input.bam + samtools view -@ \${GALAXY_SLOTS:-1} -b -o unsorted_output.bam temp_input.bam ${ ' '.join( map( lambda x:'"%s"' % ( x ), str( $slice_method.refs ).split(",") ) ) } && #elif str($slice_method.slice_method_selector) == "man": - samtools view -@ \${GALAXY_SLOTS:-1} -b -o unsorted_output.bam temp_input.bam + samtools view -@ \${GALAXY_SLOTS:-1} -b -o unsorted_output.bam temp_input.bam #for $region in $slice_method.regions: "${region.chrom}:${region.start}-${region.end}" @@ -28,7 +28,7 @@ samtools sort -O bam - -T sorted + -T "\${TMPDIR:-.}" -@ \${GALAXY_SLOTS:-1} -o '${output_bam}' unsorted_output.bam @@ -83,13 +83,13 @@ <param name="input_bam" ftype="bam" value="bam-slice-input.bam" /> <param name="slice_method_selector" value="bed"/> <param name="input_interval" ftype="bed" value="bam-slice.bed" /> - <output name="output_bam" file="bam-slice-test1.bam" ftype="bam" /> + <output name="output_bam" file="bam-slice-test1.bam" ftype="bam" lines_diff="4" /> </test> <test> <param name="input_bam" ftype="bam" value="bam-slice-input.bam" /> <param name="slice_method_selector" value="chr"/> <param name="refs" value="chrM" /> - <output name="output_bam" file="bam-slice-test2.bam" ftype="bam" /> + <output name="output_bam" file="bam-slice-test2.bam" ftype="bam" lines_diff="4" /> </test> <test> <param name="input_bam" ftype="bam" value="bam-slice-input.bam" /> @@ -97,7 +97,7 @@ <param name="chrom" value="chrM" /> <param name="start" value="1" /> <param name="end" value="1000" /> - <output name="output_bam" file="bam-slice-test3.bam" ftype="bam" /> + <output name="output_bam" file="bam-slice-test3.bam" ftype="bam" lines_diff="4"/> </test> </tests> <help><![CDATA[ @@ -106,7 +106,7 @@ Allows to restrict (slice) input BAM dataset to a list of intervals defined in a BED file, individual chromosomes, or manually set list of coordinates. BED datasets can be obtained from **Get Data -> UCSC Main**. -This tool is based on ``samtools view`` command. +This tool is based on ``samtools view`` command. @no-chrom-options@ ]]></help>