| Previous changeset 1:f5792425ea50 (2021-05-13) Next changeset 3:b226e0c805a5 (2021-08-20) |
|
Commit message:
"planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0" |
|
modified:
bam2msa.xml macros.xml test-data/bam2msa-out1.fa test-data/bealign-out1.bam |
| b |
| diff -r f5792425ea50 -r 0a4ad829d87a bam2msa.xml --- a/bam2msa.xml Thu May 13 16:57:46 2021 +0000 +++ b/bam2msa.xml Fri Jul 09 15:18:46 2021 +0000 |
| [ |
| @@ -1,35 +1,36 @@ <?xml version="1.0"?> -<tool id="bioext_bam2msa" name="Convert BAM" version="@VERSION@.0"> - <description>to FASTA multiple sequence alignment</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements"/> - <command detect_errors="exit_code"><![CDATA[ - bam2msa - #if $region_start and $region_end: - -r $region_start:$region_end - #end if - '$input' '$output' - ]]></command> - <inputs> - <param name="input" type="data" format="bam,sam" label="Input BAM file"/> - <param name="region_start" type="integer" value="0" optional="True" label="Starting coordinate" help="Leave blank to extract all sequences"/> - <param name="region_end" type="integer" value="0" optional="True" label="End coordinate"/> - </inputs> - <outputs> - <data name="output" format="fasta"/> - </outputs> - <tests> - <test> - <param name="input" ftype="bam" value="bealign-out1.bam"/> - <output name="output" file="bam2msa-out1.fa"/> - </test> - <test> - <param name="input" ftype="bam" value="bealign-out2.bam"/> - <output name="output" file="bam2msa-out2.fa"/> - </test> - </tests> - <help>Extract MSA from a BAM file</help> - <expand macro="citations"/> +<tool id="bioext_bam2msa" name="Convert BAM" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>to FASTA multiple sequence alignment</description> + <macros> + <import>macros.xml</import> + <token name="@VERSION_SUFFIX@">0</token> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ + bam2msa + #if $region_start and $region_end: + -r $region_start:$region_end + #end if + '$input' '$output' + ]]></command> + <inputs> + <param name="input" type="data" format="bam,sam" label="Input BAM file"/> + <param name="region_start" type="integer" value="0" optional="True" label="Starting coordinate" help="Leave blank to extract all sequences"/> + <param name="region_end" type="integer" value="0" optional="True" label="End coordinate"/> + </inputs> + <outputs> + <data name="output" format="fasta"/> + </outputs> + <tests> + <test> + <param name="input" ftype="bam" value="bealign-out1.bam"/> + <output name="output" file="bam2msa-out1.fa"/> + </test> + <test> + <param name="input" ftype="bam" value="bealign-out2.bam"/> + <output name="output" file="bam2msa-out2.fa"/> + </test> + </tests> + <help>Extract MSA from a BAM file</help> + <expand macro="citations"/> </tool> |
| b |
| diff -r f5792425ea50 -r 0a4ad829d87a macros.xml --- a/macros.xml Thu May 13 16:57:46 2021 +0000 +++ b/macros.xml Fri Jul 09 15:18:46 2021 +0000 |
| b |
| @@ -1,9 +1,10 @@ <?xml version="1.0"?> <macros> - <token name="@VERSION@">0.19.7</token> + <token name="@TOOL_VERSION@">0.20.1</token> + <token name="@PROFILE@">20.05</token> <xml name="requirements"> <requirements> - <requirement type="package" version="@VERSION@">python-bioext</requirement> + <requirement type="package" version="@TOOL_VERSION@">python-bioext</requirement> <yield /> </requirements> </xml> |
| b |
| diff -r f5792425ea50 -r 0a4ad829d87a test-data/bam2msa-out1.fa --- a/test-data/bam2msa-out1.fa Thu May 13 16:57:46 2021 +0000 +++ b/test-data/bam2msa-out1.fa Fri Jul 09 15:18:46 2021 +0000 |
| b |
| @@ -1,4 +1,4 @@ ->Z|JP|K03455|2036|DUPLICATE +>Z_JP_K03455_2036_DUPLICATE_2 CCTCAAATCACTCTTTGGCAACGACCCTTAGTTACAGCAAAAATAGGGGAACAGCTAATA GAAGCCCTATTAGACACAGGAGCAGATGATACAGTATTAGAAGAAATAAATTTACCAGGG AAATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAT @@ -26,7 +26,7 @@ ATATGGGGAAAGACCCCTAAATTTAGACTACCCATACAAAAAGAAACATGGGAAGCA--- ------------------------------------------------------------ --------------------------------------------------------- ->Z|JP|K03455|2036|DUPLICATE +>Z_JP_K03455_2036_DUPLICATE_3 CCTCAAATCACTCTTTGGCAACGACCCTTAGTTACAGCAAAAATAGGGGAACAGCTAATA GAAGCCCTATTAGACACAGGAGCAGATGATACAGTATTAGAAGAAATAAATTTACCAGGG AAATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAT @@ -54,7 +54,7 @@ ATATGGGGAAAGACCCCTAAATTTAGACTACCCATACAAAAAGAAACATGGGAAGCA--- ------------------------------------------------------------ --------------------------------------------------------- ->Z|JP|K03455|2036|DUPLICATE +>Z_JP_K03455_2036_DUPLICATE_4 CCTCAAATCACTCTTTGGCAACGACCCTTAGTTACAGCAAAAATAGGGGAACAGCTAATA GAAGCCCTATTAGACACAGGAGCAGATGATACAGTATTAGAAGAAATAAATTTAYCAGGG AAATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAT @@ -82,7 +82,7 @@ ATATGGGGAAAGACCCCTAAATTTAGACTACCCATACAAAAAGAAACATGGGAAGCA--- ------------------------------------------------------------ --------------------------------------------------------- ->Z|JP|K03455|2036|DUPLICATE +>Z_JP_K03455_2036_DUPLICATE_5 CCTCAAATCACTCTTTGGCAACGACCCTTAGTTACAGCAAAAATAGGGGAACAGCTAATA GAAGCCCTATTAGACACAGGAGCAGATGATACAGTATTAGAAGAAATAAATTTACCAGGG AAATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAGGTAAGACAATATGAT @@ -110,7 +110,7 @@ ------------------------------------------------------------ ------------------------------------------------------------ --------------------------------------------------------- ->Z|JP|K03455|2036|DUPLICATE +>Z_JP_K03455_2036_DUPLICATE_6 CCTCAAATCACTCTTTGGCAACGACCCTTAGTTACAGCAAAAATAGGGGAACAGCTAATA GAAGCCCTATTAGACACAGGAGCAGATGATACAGTATTAGAAGAAATAAATTTACCAGGG AAATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAATATGAT @@ -138,7 +138,7 @@ ATATGGGGAAAGACCCCTAAATTTAGACTACCCATACAAAAAGAAACATGGGAAGCA--- ------------------------------------------------------------ --------------------------------------------------------- ->Z|JP|K03455|2036|DUPLICATE +>Z_JP_K03455_2036_DUPLICATE_7 CCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAG GAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGA AGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAT @@ -166,7 +166,7 @@ ATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGG TGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCC TTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTC ->Z|JP|K03455|2036 +>Z_JP_K03455_2036 ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ |
| b |
| diff -r f5792425ea50 -r 0a4ad829d87a test-data/bealign-out1.bam |
| b |
| Binary file test-data/bealign-out1.bam has changed |