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"

--- 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>