diff fasta_extract.xml @ 0:bc3f2a5c7b53 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fasta_extract.xml	Sun Jan 10 13:03:12 2016 -0500
@@ -0,0 +1,71 @@
+<tool id="fasta_extract" name="Extract fasta sequences" version="1.0.0">
+    <description>using coordinates from assembled genomes</description>
+    <macros>
+        <import>fasta_extract_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command>
+        <![CDATA[
+            mkdir -p output_dir &&
+            python $__tool_directory__/fasta_extract.py
+            #for $i in $inputs:
+                --input "$i" "${i.hid}"
+            #end for
+            #if str($reference_genome_cond.reference_genome_source) == "cached":
+                #set genome_file = $reference_genome_cond.reference_genome.fields.path
+            #else:
+                #set genome_file = $reference_genome_cond.reference_genome
+            #end if
+            --genome_file "$genome_file"
+            --subtract_from_start $subtract_from_start
+            --add_to_end $add_to_end
+            --extend_existing $extend_existing
+            --strand $strand
+        ]]>
+    </command>
+    <inputs>
+        <param name="inputs" type="data" format="gff" multiple="True" label="Fetch sequences for intervals in">
+            <validator type="unspecified_build" />
+        </param>
+        <conditional name="reference_genome_cond">
+            <param name="reference_genome_source" type="select" label="Choose the source for the reference genome">
+                <option value="cached">Locally Cached</option>
+                <option value="history">From History</option>
+            </param>
+            <when value="cached">
+                <param name="reference_genome" type="select" label="Using reference genome">
+                    <options from_data_table="all_fasta" />
+                    <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
+                </param>
+            </when>
+            <when value="history">
+                <param name="reference_genome" type="data" format="fasta" label="Using reference genome"/>
+            </when>
+        </conditional>
+        <param name="subtract_from_start" type="integer" value="50" min="0" label="Distance to subtract from start" />
+        <param name="add_to_end" type="integer" value="50" min="0" label="Distance to add to end" />
+        <param name="extend_existing" type="select" label="Extend existing start and end coordinates or extend from computed midpoint?">
+            <option value="midpoint" selected="True">Extend from computed midpoint</option>
+            <option value="existing">Extend from existing start and end coordinates</option>
+        </param>
+        <param name="strand" type="select" label="Extract reverse complement sequence on reverse strand?">
+            <option value="no" selected="True">No</option>
+            <option value="yes">Yes</option>
+        </param>
+    </inputs>
+    <outputs>
+        <collection name="fasta_extract_output" type="list" label="Extract fasta sequences ${on_string}">
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="output_dir" ext="fasta" visible="false" />
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+        </test>
+    </tests>
+    <help>
+
+**What it does**
+
+   </help>
+   <expand macro="citations" />
+</tool>