diff get_reference_fasta.xml @ 0:e30b3bc5b344 draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit 98d53eb3a7a5f53f3779dbd8e0508c8c3dd338cf"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_reference_fasta.xml	Tue Jan 07 09:05:46 2020 +0000
@@ -0,0 +1,30 @@
+<tool id="get_fasta_reference" name="get fasta reference"  version="0.2.1">
+<description>Obtain reference genome sequence</description>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <command><![CDATA[
+        cat "$pre_installed_fasta.fields.path" > "$output"
+    ]]></command>
+    <inputs>
+          <param help="if you wish to have your fasta sequence listed contact instance administrator" label="Select a fasta sequence" name="pre_installed_fasta" type="select">
+          <options from_data_table="all_fasta"/>
+          </param>
+    </inputs>
+    <outputs>
+        <data name="output" label="${pre_installed_fasta.value_label}" format="fasta" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="pre_installed_fasta" value="EcR_USP_224.fa"/>
+            <output name="output" file="EcR_USP_224.fa"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+Places the reference genome sequence in the current history.    
+Useful for sharing purposes or tools that work directly on fasta files.
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1186/gb-2010-11-8-r86</citation>
+    </citations>
+</tool>