Mercurial > repos > peterjc > seq_rename

changeset 13:d08767ae73ce draft

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Uploaded v0.0.4i, depend on Biopython 1.62
author peterjc
date Fri, 27 Sep 2013 06:10:29 -0400
parents 311012138753
children 61cec46f6be5
files tools/seq_rename/repository_dependencies.xml tools/seq_rename/seq_rename.xml
diffstat 2 files changed, 53 insertions(+), 54 deletions(-) [+]
line wrap: on
line diff
--- a/tools/seq_rename/repository_dependencies.xml	Thu Sep 26 10:07:49 2013 -0400
+++ b/tools/seq_rename/repository_dependencies.xml	Fri Sep 27 06:10:29 2013 -0400
@@ -2,5 +2,5 @@
 <repositories description="This requires Biopython as a dependency.">
 <!-- Leave out the tool shed and revision to get the current
      tool shed and latest revision at the time of upload -->
-<repository changeset_revision="2f6c871cfa35" name="package_biopython_1_61" owner="biopython" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+<repository changeset_revision="ac9cc2992b69" name="package_biopython_1_62" owner="biopython" toolshed="http://testtoolshed.g2.bx.psu.edu" />
 </repositories>
--- a/tools/seq_rename/seq_rename.xml	Thu Sep 26 10:07:49 2013 -0400
+++ b/tools/seq_rename/seq_rename.xml	Fri Sep 27 06:10:29 2013 -0400
@@ -1,62 +1,61 @@
 <tool id="seq_rename" name="Rename sequences" version="0.0.4">
-	<description>with ID mapping from a tabular file</description>
-	<requirements>
-		<requirement type="package" version="1.61">biopython</requirement>
-		<requirement type="python-module">Bio</requirement>
-	</requirements>
-	<version_commmand interpreter="python">seq_rename.py --version</version_commmand>
-	<command interpreter="python">
+    <description>with ID mapping from a tabular file</description>
+    <requirements>
+        <requirement type="package" version="1.62">biopython</requirement>
+        <requirement type="python-module">Bio</requirement>
+    </requirements>
+    <version_commmand interpreter="python">seq_rename.py --version</version_commmand>
+    <command interpreter="python">
 seq_rename.py $input_tabular $old_column $new_column $input_file $input_file.ext $output_file
-	</command>
-	<stdio>
-		<!-- Anything other than zero is an error -->
-		<exit_code range="1:" />
-		<exit_code range=":-1" />
-	</stdio>
-	<inputs>
-		<param name="input_file" type="data" format="fasta,qual,fastq,sff" label="Sequence file" help="FASTA, QUAL, FASTQ, or SFF format." />
-		<param name="input_tabular" type="data" format="tabular" label="Tabular file containing sequence identifiers"/>
-		<param name="old_column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing current (old) sequence identifiers"/>
-                <param name="new_column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing new sequence identifiers"/>
-	</inputs>
-	<outputs>
-		<data name="output_file" format="fasta" label="Renamed ${on_string}">
-			<!-- TODO - Replace this with format="input:input_fastq" if/when that works -->
-			<change_format>
-				<when input_dataset="input_file" attribute="extension" value="sff" format="sff" />
-				<when input_dataset="input_file" attribute="extension" value="fastq" format="fastq" />
-				<when input_dataset="input_file" attribute="extension" value="fastqsanger" format="fastqsanger" />
-				<when input_dataset="input_file" attribute="extension" value="fastqsolexa" format="fastqsolexa" />
-				<when input_dataset="input_file" attribute="extension" value="fastqillumina" format="fastqillumina" />
-				<when input_dataset="input_file" attribute="extension" value="fastqcssanger" format="fastqcssanger" />
-			</change_format>
-		</data>
-	</outputs>
-	<tests>
-		<test>
-			<param name="input_file" value="four_human_proteins.fasta" ftype="fasta" />
-			<param name="input_tabular" value="four_human_proteins.rename.tabular" ftype="tabular" />
-			<param name="old_column" value="1" />
-			<param name="new_column" value="2" />
-			<output name="output_file" file="four_human_proteins.rename.fasta" ftype="fasta" />
-		</test>
-		<test>
-			<param name="input_file" value="four_human_proteins.fasta" ftype="fasta" />
-			<param name="input_tabular" value="four_human_proteins.rename.tabular" ftype="tabular" />
-			<param name="old_column" value="c1" />
-			<param name="new_column" value="c2" />
-			<output name="output_file" file="four_human_proteins.rename.fasta" ftype="fasta" />
-		</test>
-	</tests>
-	<help>
-
+    </command>
+    <stdio>
+        <!-- Anything other than zero is an error -->
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
+    <inputs>
+        <param name="input_file" type="data" format="fasta,qual,fastq,sff" label="Sequence file" help="FASTA, QUAL, FASTQ, or SFF format." />
+        <param name="input_tabular" type="data" format="tabular" label="Tabular file containing sequence identifiers"/>
+        <param name="old_column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing current (old) sequence identifiers"/>
+        <param name="new_column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing new sequence identifiers"/>
+    </inputs>
+    <outputs>
+        <data name="output_file" format="fasta" label="Renamed ${on_string}">
+            <!-- TODO - Replace this with format="input:input_fastq" if/when that works -->
+            <change_format>
+                <when input_dataset="input_file" attribute="extension" value="sff" format="sff" />
+		<when input_dataset="input_file" attribute="extension" value="fastq" format="fastq" />
+		<when input_dataset="input_file" attribute="extension" value="fastqsanger" format="fastqsanger" />
+		<when input_dataset="input_file" attribute="extension" value="fastqsolexa" format="fastqsolexa" />
+		<when input_dataset="input_file" attribute="extension" value="fastqillumina" format="fastqillumina" />
+		<when input_dataset="input_file" attribute="extension" value="fastqcssanger" format="fastqcssanger" />
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" />
+            <param name="input_tabular" value="four_human_proteins.rename.tabular" ftype="tabular" />
+            <param name="old_column" value="1" />
+            <param name="new_column" value="2" />
+            <output name="output_file" file="four_human_proteins.rename.fasta" ftype="fasta" />
+        </test>
+        <test>
+            <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" />
+            <param name="input_tabular" value="four_human_proteins.rename.tabular" ftype="tabular" />
+            <param name="old_column" value="c1" />
+            <param name="new_column" value="c2" />
+            <output name="output_file" file="four_human_proteins.rename.fasta" ftype="fasta" />
+        </test>
+    </tests>
+    <help>
 **What it does**
 
 Takes a FASTA, QUAL, FASTQ or Standard Flowgram Format (SFF) file and produces a
 new sequence file (of the same format) where the sequence identifiers have been
-renamed according two the specified columns a the tabular file.
+renamed according to the specified columns in your tabular file.
 
-WARNING: If you have any duplicates in the intput sequence file, you will still
+WARNING: If you have any duplicates in the input sequence file, you will still
 have duplicate sequences in the output.
 
 WARNING: If the tabular file has more than one new name for any old ID, the
@@ -81,5 +80,5 @@
 
 This tool is available to install into other Galaxy Instances via the Galaxy
 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/seq_rename
-	</help>
+    </help>
 </tool>