diff data_manager/novoalign_index_builder.xml @ 0:85fbd52dbb36 draft

planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/novoalign_index_builder.xml	Thu Mar 03 05:59:41 2016 -0500
@@ -0,0 +1,53 @@
+<?xml version="1.0" encoding="utf-8" ?>
+<tool id="novoalign_index_builder" name="NOVO ALIGN index" version="0.0.1">
+    <description>Build an index for use by the Novo Align mapping tool</description>
+    <requirements>
+        <requirement type="package" version="0.0.1d">novoalign</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range=":-1" />
+        <exit_code range="1:" />
+    </stdio>
+    <command interpreter="python">
+        novoalign_index_builder.py "${out_file}" --data_table_name "novo_index"
+    </command>
+    <inputs>
+        <conditional name="reference_source">
+          <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
+            <option value="url">URL</option>
+            <option value="history">History</option>
+            <option value="directory">Directory on Server</option>
+          </param>
+          <when value="url">
+            <param type="text" area="True" name="user_url" value="http://" label="URLs" optional="False" />
+          </when>
+          <when value="history">
+            <param name="input_fasta" type="data" format="fasta" label="FASTA File" multiple="False" optional="False" />
+          </when>
+          <when value="directory">
+            <param type="text" name="fasta_filename" value="" label="Full path to FASTA File on disk" optional="False" />
+            <param type="boolean" name="create_symlink" truevalue="create_symlink" falsevalue="copy_file" label="Create symlink to orignal data instead of copying" checked="False" />
+          </when>
+        </conditional>
+        <!-- <param type="text" name="sequence_name" value="" label="Name of sequence" />
+        <param type="text" name="sequence_id" value="" label="ID for sequence" /> -->
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="dbkey" value="anoGam1"/>
+            <param name="sequence_name" value=""/>
+            <param name="sequence_id" value=""/>
+            <param name="reference_source_selector" value="history"/>
+            <param name="input_fasta" value="phiX174.fasta"/>
+            <param name="sort_selector" value="as_is"/>
+            <output name="out_file" file="phiX174_as_anoGam1.data_manager_json"/>
+        </test>
+    </tests>
+    <help>Help!</help>
+    <citations>
+        <citation></citation>
+    </citations>
+</tool>