Mercurial > repos > iuc > crossmap_bam

changeset 3:cb3557cabc7b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 23fab16cd40acbd5b0e9d640ed3858040db7a622
author iuc
date Thu, 24 May 2018 19:10:46 -0400
parents 083774cc8472
children 5051467dc96a
files crossmap_bam.xml macros.xml
diffstat 2 files changed, 7 insertions(+), 11 deletions(-) [+]
line wrap: on
line diff
--- a/crossmap_bam.xml	Fri Oct 20 11:33:02 2017 -0400
+++ b/crossmap_bam.xml	Thu May 24 19:10:46 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="crossmap_bam" name="CrossMap BAM" version="@WRAPPER_VERSION@-0">
+<tool id="crossmap_bam" name="CrossMap BAM" version="@WRAPPER_VERSION@">
     <description>Convert genome coordinates or annotation files between genome assemblies</description>
     <macros>
         <import>macros.xml</import>
@@ -7,7 +7,6 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-
 CrossMap.py bam
 '${chain_source.input_chain}'
 $optional_tags
@@ -17,9 +16,7 @@
 -t $insert_size_fold
 
 '${input}'
-'${output}'
-
-&& mv '${output}.sorted.bam' '${output}'
+output
     ]]></command>
     <inputs>
         <param name="input" type="data" format="bam" label="BAM file"/>
@@ -34,7 +31,7 @@
     </inputs>
 
     <outputs>
-        <data name="output" format="bam" label="${tool.name} on ${on_string}" />
+        <data name="output" format="bam" label="${tool.name} on ${on_string}" from_work_dir="output.sorted.bam" />
         <!-- CrossMap 0.2.5 does not produce output_unmapped -->
     </outputs>
 
@@ -45,7 +42,7 @@
             <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
             <param name="include_fails" value="False"/>
 
-            <output name="output" file="test_bam_01_output_a.bam" compare="diff" lines_diff="8"/>
+            <output name="output" file="test_bam_01_output_a.bam" ftype="bam" />
         </test>
         <test>
             <param name="index_source" value="cached"/>
@@ -53,7 +50,7 @@
             <param name="input" value="test_bam_01_input_a.bam" ftype="bam" dbkey="hg18"/>
             <param name="include_fails" value="False"/>
 
-            <output name="output" file="test_bam_01_output_a.bam" compare="diff" lines_diff="8"/>
+            <output name="output" file="test_bam_01_output_a.bam" ftype="bam" />
         </test>
     </tests>
     <help><![CDATA[
@@ -115,7 +112,6 @@
     multiple mapped
 SU
     uniquely mapped
-
     ]]></help>
 
     <citations>
--- a/macros.xml	Fri Oct 20 11:33:02 2017 -0400
+++ b/macros.xml	Thu May 24 19:10:46 2018 -0400
@@ -2,11 +2,11 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="0.2.5">crossmap</requirement>
+            <requirement type="package" version="0.2.7">crossmap</requirement>
             <yield/>
         </requirements>
     </xml>
-    <token name="@WRAPPER_VERSION@">0.2.5</token>
+    <token name="@WRAPPER_VERSION@">0.2.7</token>
     <xml name="stdio">
         <stdio>
             <regex match="Aborted (core dumped)" source="stdout" level="fatal"/>