| Previous changeset 19:dfd8b7f78c37 (2017-12-22) Next changeset 21:8d2a528a9513 (2018-04-10) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 4a306ebd8b7808ce963a69a3b15dd860c1fde585 |
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modified:
bwa-mem.xml bwa.xml bwa_macros.xml |
| b |
| diff -r dfd8b7f78c37 -r 4f774c1e6049 bwa-mem.xml --- a/bwa-mem.xml Fri Dec 22 15:03:03 2017 -0500 +++ b/bwa-mem.xml Thu Feb 01 12:35:35 2018 -0500 |
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| @@ -7,8 +7,7 @@ </macros> <expand macro="requirements"/> <expand macro="stdio"/> - <command> -<![CDATA[ + <command><![CDATA[ @set_reference_fasta_filename@ ## Begin BWA-MEM command line @@ -107,8 +106,7 @@ #end if | samtools sort -@\${GALAXY_SLOTS:-2} -O bam -o '$bam_output' -]]> - </command> + ]]></command> <inputs> <expand macro="reference_source_conditional" /> |
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| diff -r dfd8b7f78c37 -r 4f774c1e6049 bwa.xml --- a/bwa.xml Fri Dec 22 15:03:03 2017 -0500 +++ b/bwa.xml Thu Feb 01 12:35:35 2018 -0500 |
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| @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="bwa" name="Map with BWA" version="@VERSION@.3"> +<tool id="bwa" name="Map with BWA" version="@VERSION@.4"> <description>- map short reads (< 100 bp) against reference genome</description> <macros> <import>read_group_macros.xml</import> @@ -305,7 +305,7 @@ </inputs> <outputs> <data format="bam" name="bam_output" label="${tool.name} on ${on_string} (mapped reads in BAM format)"> - <expand macro="dbKeyActionsBwa"/> + <expand macro="dbKeyActionsBwaMem"/> </data> </outputs> <tests> |
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| diff -r dfd8b7f78c37 -r 4f774c1e6049 bwa_macros.xml --- a/bwa_macros.xml Fri Dec 22 15:03:03 2017 -0500 +++ b/bwa_macros.xml Thu Feb 01 12:35:35 2018 -0500 |
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| @@ -75,15 +75,6 @@ </conditional> </macro> - <macro name="dbKeyActionsBwa"> - <expand macro="dbKeyActions"> - <option type="from_data_table" name="bwa_indexes" column="1" offset="0"> - <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> - <filter type="param_value" ref="reference_source.ref_file" column="0"/> - </option> - </expand> - </macro> - <macro name="dbKeyActionsBwaMem"> <expand macro="dbKeyActions"> <option type="from_data_table" name="bwa_mem_indexes" column="1" offset="0"> |