Mercurial > repos > devteam > tabular_to_fasta

diff tabular_to_fasta.xml @ 1:7f7a1bea4653 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/tabular_to_fasta commit 01140c0ac1a926856c55853a0028e5d44935d9e6"
author devteam
date Wed, 05 Feb 2020 15:51:26 +0000
parents db61adc12770
children
line wrap: on
line diff
--- a/tabular_to_fasta.xml	Mon May 19 10:59:53 2014 -0400
+++ b/tabular_to_fasta.xml	Wed Feb 05 15:51:26 2020 +0000
@@ -1,43 +1,50 @@
-<tool id="tab2fasta" name="Tabular-to-FASTA" version="1.1.0">
-	<description>converts tabular file to FASTA format</description>
-	<command interpreter="python">tabular_to_fasta.py $input $title_col $seq_col $output </command>
-	<inputs>
-		<param name="input" type="data" format="tabular" label="Tab-delimited file"/>
-		<param name="title_col" type="data_column" data_ref="input" multiple="True" numerical="False" label="Title column(s)" help="Multi-select list - hold the appropriate key while clicking to select multiple columns"/>
-		<param name="seq_col" type="data_column" data_ref="input" numerical="False" label="Sequence column" />
-	</inputs>
-	<outputs>
-		<data name="output" format="fasta"/>
-	</outputs>
-	<tests>
-		<test>
-			<param name="input" value="solexa.tabular" />
-			<param name="title_col" value="1,2,3,4" />
-			<param name="seq_col" value="5" />
-			<output name="output" file="tabular_to_fasta_out1.fasta" />
-		</test>
-	</tests>
-	<help>
-	
+<tool id="tab2fasta" name="Tabular-to-FASTA" version="1.1.1" profile="16.04">
+    <description>converts tabular file to FASTA format</description>
+    <requirements>
+        <requirement type="package" version="3.7">python</requirement>
+    </requirements>
+    <command><![CDATA[
+python '$__tool_directory__/tabular_to_fasta.py'
+'$input'
+$title_col
+$seq_col
+'$output'
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="tabular" label="Tab-delimited file"/>
+        <param name="title_col" type="data_column" data_ref="input" multiple="true" numerical="false" label="Title column(s)" help="Multi-select list - hold the appropriate key while clicking to select multiple columns"/>
+        <param name="seq_col" type="data_column" data_ref="input" numerical="false" label="Sequence column" />
+    </inputs>
+    <outputs>
+        <data name="output" format="fasta"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="solexa.tabular" />
+            <param name="title_col" value="1,2,3,4" />
+            <param name="seq_col" value="5" />
+            <output name="output" file="tabular_to_fasta_out1.fasta" />
+        </test>
+    </tests>
+    <help><![CDATA[
 **What it does**
 
 Converts tab delimited data into FASTA formatted sequences.
 
 -----------
-	
+
 **Example**
 
 Suppose this is a sequence file produced by Illumina (Solexa) sequencer::
 
-	5	300	902	419	GACTCATGATTTCTTACCTATTAGTGGTTGAACATC
-	5	300	880	431	GTGATATGTATGTTGACGGCCATAAGGCTGCTTCTT
-	
+    5	300	902	419	GACTCATGATTTCTTACCTATTAGTGGTTGAACATC
+    5	300	880	431	GTGATATGTATGTTGACGGCCATAAGGCTGCTTCTT
+
 Selecting **c3** and **c4** as the **Title column(s)** and **c5** as the **Sequence column** will result in::
 
-	&gt;902_419
-	GACTCATGATTTCTTACCTATTAGTGGTTGAACATC
-	&gt;880_431
-	GTGATATGTATGTTGACGGCCATAAGGCTGCTTCTT
-	
-	</help>
-</tool>
\ No newline at end of file
+    >902_419
+    GACTCATGATTTCTTACCTATTAGTGGTTGAACATC
+    >880_431
+    GTGATATGTATGTTGACGGCCATAAGGCTGCTTCTT
+    ]]></help>
+</tool>