# HG changeset patch
# User peterjc
# Date 1380276891 14400
# Node ID 9e9e3b860aa0b65d60603bd60cc95459d589748f
# Parent  726dcfa94b2cacfd8cae5c17f47b4b1e3af1edbf
Uploaded v0.0.7e, depend on Biopython 1.62, tabs to spaces in XML

diff -r 726dcfa94b2c -r 9e9e3b860aa0 tools/seq_select_by_id/repository_dependencies.xml
--- a/tools/seq_select_by_id/repository_dependencies.xml	Thu Sep 26 10:09:17 2013 -0400
+++ b/tools/seq_select_by_id/repository_dependencies.xml	Fri Sep 27 06:14:51 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>
diff -r 726dcfa94b2c -r 9e9e3b860aa0 tools/seq_select_by_id/seq_select_by_id.xml
--- a/tools/seq_select_by_id/seq_select_by_id.xml	Thu Sep 26 10:09:17 2013 -0400
+++ b/tools/seq_select_by_id/seq_select_by_id.xml	Fri Sep 27 06:14:51 2013 -0400
@@ -1,46 +1,45 @@
 <tool id="seq_select_by_id" name="Select sequences by ID" version="0.0.6">
-	<description>from a tabular file</description>
-	<requirements>
-		<requirement type="package" version="1.61">biopython</requirement>
-		<requirement type="python-module">Bio</requirement>
-	</requirements>
-	<version_command interpreter="python">seq_select_by_id.py --version</version_command>
-	<command interpreter="python">
+    <description>from a tabular file</description>
+    <requirements>
+        <requirement type="package" version="1.62">biopython</requirement>
+        <requirement type="python-module">Bio</requirement>
+    </requirements>
+    <version_command interpreter="python">seq_select_by_id.py --version</version_command>
+    <command interpreter="python">
 seq_select_by_id.py $input_tabular $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 to select from" help="FASTA, QUAL, FASTQ, or SFF format." />
-		<param name="input_tabular" type="data" format="tabular" label="Tabular file containing sequence identifiers"/>
-		<param name="column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing sequence identifiers"/>
-	</inputs>
-	<outputs>
-		<data name="output_file" format="fasta" label="Selected sequences">
-			<!-- 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="k12_ten_proteins.fasta" ftype="fasta" />
-			<param name="input_tabular" value="k12_hypothetical.tabular" ftype="tabular" />
-			<param name="column" value="1" />
-			<output name="output_file" file="k12_hypothetical.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 to select from" help="FASTA, QUAL, FASTQ, or SFF format." />
+        <param name="input_tabular" type="data" format="tabular" label="Tabular file containing sequence identifiers"/>
+        <param name="column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing sequence identifiers"/>
+    </inputs>
+    <outputs>
+        <data name="output_file" format="fasta" label="Selected sequences">
+            <!-- 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="k12_ten_proteins.fasta" ftype="fasta" />
+            <param name="input_tabular" value="k12_hypothetical.tabular" ftype="tabular" />
+            <param name="column" value="1" />
+            <output name="output_file" file="k12_hypothetical.fasta" ftype="fasta" />
+        </test>
+    </tests>
+    <help>
 **What it does**
 
 Takes a FASTA, QUAL, FASTQ or Standard Flowgram Format (SFF) file and produces a
@@ -69,5 +68,5 @@
 
 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_select_by_id
-	</help>
+    </help>
 </tool>