Mercurial > repos > rplanel > sequence_splitter

changeset 2:6dd4f53b9964 draft default tip

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"planemo upload for repository https://github.com/rplanel/galaxy-tools/tree/master/tools/sequence-splitter commit 98f957247a46eabf7e561bd94328b6a03a4d73b9"
author rplanel
date Sat, 21 Nov 2020 08:50:21 +0000
parents 7b509a1801e4
children
files macros.xml sequence-splitter.py sequence-splitter.xml
diffstat 3 files changed, 51 insertions(+), 41 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Tue Aug 20 09:46:49 2019 -0400
+++ b/macros.xml	Sat Nov 21 08:50:21 2020 +0000
@@ -1,5 +1,14 @@
 <?xml version='1.0' encoding='UTF-8'?>
 <macros>
+    <token name="@WRAPPER_VERSION@">1.0.0</token>
+
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="3.8.1">python</requirement>
+            <requirement type="package" version="1.78">biopython</requirement>
+            <yield />
+        </requirements>
+    </xml>
     <xml name="citations">
         <citations>
             <citation type="bibtex">
--- a/sequence-splitter.py	Tue Aug 20 09:46:49 2019 -0400
+++ b/sequence-splitter.py	Sat Nov 21 08:50:21 2020 +0000
@@ -1,4 +1,4 @@
-#!/usr/bin/env python2
+#!/usr/bin/env python3
 # coding: utf-8
 
 import argparse
--- a/sequence-splitter.xml	Tue Aug 20 09:46:49 2019 -0400
+++ b/sequence-splitter.xml	Sat Nov 21 08:50:21 2020 +0000
@@ -1,11 +1,8 @@
-<tool id="sequence-splitter" name="Sequence Splitter" version="0.1.1">
+<tool id="sequence-splitter" name="Sequence Splitter" version="@WRAPPER_VERSION@">
     <macros>
         <import>macros.xml</import>
     </macros>
-    <requirements>
-        <requirement type="package" version="2.7.11">python</requirement>
-        <requirement type="package" version="1.73">biopython</requirement>
-    </requirements>
+    <expand macro="requirements" />
     <edam_operations>
         <edam_operation>operation_2409</edam_operation>
         <edam_operation>operation_3359</edam_operation>
@@ -14,7 +11,8 @@
         <edam_topic>topic_3307</edam_topic>
         <edam_topic>topic_0080</edam_topic>
     </edam_topics>
-    <command detect_errors="exit_code"><![CDATA[
+    <command detect_errors="exit_code">
+        <![CDATA[
         ln -s '$sequences' ./sequences.${sequences.ext} &&
         python 
             '$__tool_directory__/sequence-splitter.py' 
@@ -30,19 +28,20 @@
                 -n $split_mode.nb_chunk
             #end if
             -o 'outputs'
-    ]]>    </command>
+    ]]>
+    </command>
     <inputs>
-        <param type="data" name="sequences" format="fasta,fastq"/>
+        <param type="data" name="sequences" format="fasta,fastq" />
         <conditional name="split_mode">
             <param name="selector" type="select" label="Split by:">
                 <option value="chunk_size">Number of sequence(s) by chunk</option>
                 <option value="nb_chunk">Number of chunk(s)</option>
             </param>
             <when value="chunk_size">
-                <param name="chunk_size" label="Chunk size" type="integer" min="1" value="100" help="How many sequences by chunk ?"/>
+                <param name="chunk_size" label="Chunk size" type="integer" min="1" value="100" help="How many sequences by chunk ?" />
             </when>
             <when value="nb_chunk">
-                <param name="nb_chunk" label="Number of chunks" type="integer" min="1" value="10" help="How many chunks ?"/>
+                <param name="nb_chunk" label="Number of chunks" type="integer" min="1" value="10" help="How many chunks ?" />
             </when>
         </conditional>
     </inputs>
@@ -50,75 +49,76 @@
         <collection name="split_output" type="list" label="splitted sequences">
             <discover_datasets pattern="(?P&lt;designation&gt;\w+-chunk-\d+)\.(?P&lt;ext&gt;.+)" directory="outputs" />
         </collection>
-        <data format="text" name="logfile" from_work_dir="sequence-splitter.log" label="${tool.name} logfile on ${on_string}"/>
+        <data format="txt" name="logfile" from_work_dir="sequence-splitter.log" label="${tool.name} logfile on ${on_string}" />
     </outputs>
     <tests>
         <!-- CHUNK SIZE -->
         <test>
-            <param name="sequences" value="sample.fastq"/>
+            <param name="sequences" value="sample.fastq" />
             <conditional name="split_mode">
-                <param name="selector" value="chunk_size"/>
-                <param name="chunk_size" value="2"/>
+                <param name="selector" value="chunk_size" />
+                <param name="chunk_size" value="2" />
             </conditional>
             <output_collection name="split_output" type="list" count="5">
-                <element name="sequences-chunk-1" file="sample-chunk-1.fastq" ftype="fastqsanger" compare="diff"/>
-                <element name="sequences-chunk-2" file="sample-chunk-2.fastq" ftype="fastqsanger" compare="diff"/>
-                <element name="sequences-chunk-3" file="sample-chunk-3.fastq" ftype="fastqsanger" compare="diff"/>
-                <element name="sequences-chunk-4" file="sample-chunk-4.fastq" ftype="fastqsanger" compare="diff"/>
-                <element name="sequences-chunk-5" file="sample-chunk-5.fastq" ftype="fastqsanger" compare="diff"/>
+                <element name="sequences-chunk-1" file="sample-chunk-1.fastq" ftype="fastqsanger" compare="diff" />
+                <element name="sequences-chunk-2" file="sample-chunk-2.fastq" ftype="fastqsanger" compare="diff" />
+                <element name="sequences-chunk-3" file="sample-chunk-3.fastq" ftype="fastqsanger" compare="diff" />
+                <element name="sequences-chunk-4" file="sample-chunk-4.fastq" ftype="fastqsanger" compare="diff" />
+                <element name="sequences-chunk-5" file="sample-chunk-5.fastq" ftype="fastqsanger" compare="diff" />
             </output_collection>
         </test>
         <test>
-            <param name="sequences" value="sample.fasta"/>
+            <param name="sequences" value="sample.fasta" />
             <conditional name="split_mode">
                 <param name="selector" value="chunk_size" />
-                <param name="chunk_size" value="5"/>
+                <param name="chunk_size" value="5" />
             </conditional>
             <output_collection name="split_output" type="list" count="1">
-                <element name="sequences-chunk-1" file="sample-5-chunk-1.fasta" ftype="fasta" compare="diff"/>
+                <element name="sequences-chunk-1" file="sample-5-chunk-1.fasta" ftype="fasta" compare="diff" />
             </output_collection>
         </test>
         <!-- NUMBER CHUNK -->
         <test>
-            <param name="sequences" value="sample.fastq"/>
+            <param name="sequences" value="sample.fastq" />
             <conditional name="split_mode">
                 <param name="selector" value="nb_chunk" />
-                <param name="nb_chunk" value="2"/>
+                <param name="nb_chunk" value="2" />
             </conditional>
             <output_collection name="split_output" type="list" count="2">
-                <element name="sequences-chunk-1" file="sample-3-chunk-1.fastq" ftype="fastqsanger" compare="diff"/>
-                <element name="sequences-chunk-2" file="sample-3-chunk-2.fastq" ftype="fastqsanger" compare="diff"/>
+                <element name="sequences-chunk-1" file="sample-3-chunk-1.fastq" ftype="fastqsanger" compare="diff" />
+                <element name="sequences-chunk-2" file="sample-3-chunk-2.fastq" ftype="fastqsanger" compare="diff" />
             </output_collection>
         </test>
         <test>
-            <param name="sequences" value="sample.fastq"/>
+            <param name="sequences" value="sample.fastq" />
             <conditional name="split_mode">
                 <param name="selector" value="nb_chunk" />
-                <param name="nb_chunk" value="4"/>
+                <param name="nb_chunk" value="4" />
             </conditional>
             <output_collection name="split_output" type="list" count="4">
-                <element name="sequences-chunk-1" file="sample-4-chunk-1.fastq" ftype="fastqsanger" compare="diff"/>
-                <element name="sequences-chunk-2" file="sample-4-chunk-2.fastq" ftype="fastqsanger" compare="diff"/>
-                <element name="sequences-chunk-3" file="sample-4-chunk-3.fastq" ftype="fastqsanger" compare="diff"/>
-                <element name="sequences-chunk-4" file="sample-4-chunk-4.fastq" ftype="fastqsanger" compare="diff"/>
+                <element name="sequences-chunk-1" file="sample-4-chunk-1.fastq" ftype="fastqsanger" compare="diff" />
+                <element name="sequences-chunk-2" file="sample-4-chunk-2.fastq" ftype="fastqsanger" compare="diff" />
+                <element name="sequences-chunk-3" file="sample-4-chunk-3.fastq" ftype="fastqsanger" compare="diff" />
+                <element name="sequences-chunk-4" file="sample-4-chunk-4.fastq" ftype="fastqsanger" compare="diff" />
             </output_collection>
         </test>
         <test>
-            <param name="sequences" value="sample.fasta"/>
+            <param name="sequences" value="sample.fasta" />
             <conditional name="split_mode">
                 <param name="selector" value="nb_chunk" />
-                <param name="nb_chunk" value="10"/>
+                <param name="nb_chunk" value="10" />
             </conditional>
             <output_collection name="split_output" type="list" count="4">
-                <element name="sequences-chunk-1" file="sample-2-chunk-1.fasta" ftype="fasta" compare="diff"/>
-                <element name="sequences-chunk-2" file="sample-2-chunk-2.fasta" ftype="fasta" compare="diff"/>
-                <element name="sequences-chunk-3" file="sample-2-chunk-3.fasta" ftype="fasta" compare="diff"/>
-                <element name="sequences-chunk-4" file="sample-2-chunk-4.fasta" ftype="fasta" compare="diff"/>
+                <element name="sequences-chunk-1" file="sample-2-chunk-1.fasta" ftype="fasta" compare="diff" />
+                <element name="sequences-chunk-2" file="sample-2-chunk-2.fasta" ftype="fasta" compare="diff" />
+                <element name="sequences-chunk-3" file="sample-2-chunk-3.fasta" ftype="fasta" compare="diff" />
+                <element name="sequences-chunk-4" file="sample-2-chunk-4.fasta" ftype="fasta" compare="diff" />
             </output_collection>
         </test>
 
     </tests>
-    <help><![CDATA[
+    <help>
+        <![CDATA[
 Usage:
 
     sequence-splitter.py [-h] [-s SEQUENCES] [-f FORMAT] (-c CHUNK_SIZE | -n NB_CHUNK) [-o OUTPUT]
@@ -144,6 +144,7 @@
                     The output directory where the chunks will be saved
 
 
-    ]]>    </help>
+    ]]>
+    </help>
     <expand macro="citations" />
 </tool>
\ No newline at end of file