diff filter_by_fasta_ids.xml @ 1:8d15aebf55fd draft

planemo upload commit 88309fbfadbafe82f2d8fb7b96468799f2421e30

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filter_by_fasta_ids.xml	Tue May 24 13:05:22 2016 -0400
@@ -0,0 +1,40 @@
+<tool id="filter_by_fasta_ids" version="1.0" name="Filter by FASTA IDs">
+    <description>Extract sequences from a FASTA file based on a list of IDs</description>
+    <command>
+<![CDATA[
+        python $__tool_directory__/filter_by_fasta_ids.py
+            $dedup
+            '$identifiers'
+            '$input'
+            '$output'
+]]>
+    </command>
+    <inputs>
+        <param format="fasta" name="input" type="data" label="FASTA sequences"/>
+        <param format="txt" name="identifiers" type="data" label="List of IDs to extract sequences for"/>
+        <param name="dedup" type="boolean" truevalue="--dedup" falsevalue="" checked="true" label="Remove duplicate sequences" />
+    </inputs>
+    <outputs>
+        <data format="fasta" name="output" label="FASTA sequences for ${identifiers.name}"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" ftype="fasta" value="input.fasta" />
+            <param name="identifiers" ftype="txt" value="ids.txt" />
+            <output name="output" file="output_dedup.fasta" />
+        </test>
+        <test>
+            <param name="input" ftype="fasta" value="input.fasta" />
+            <param name="identifiers" ftype="txt" value="ids.txt" />
+            <param name="dedup" value="False" />
+            <output name="output" file="output_not_dedup.fasta" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**What it does**
+
+Extract sequences from a FASTA file based on a list of IDs.
+]]>
+    </help>
+</tool>