Mercurial > repos > iuc > bioext_bam2msa

changeset 2:0a4ad829d87a draft

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"planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
author iuc
date Fri, 09 Jul 2021 15:18:46 +0000
parents f5792425ea50
children b226e0c805a5
files bam2msa.xml macros.xml test-data/bam2msa-out1.fa test-data/bealign-out1.bam
diffstat 4 files changed, 44 insertions(+), 42 deletions(-) [+]
line wrap: on
line diff
--- 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>
--- a/macros.xml	Thu May 13 16:57:46 2021 +0000
+++ b/macros.xml	Fri Jul 09 15:18:46 2021 +0000
@@ -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>
--- 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
@@ -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
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
Binary file test-data/bealign-out1.bam has changed