diff transtermhp.xml @ 0:c28817831a24 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/transtermhp.xml	Fri Oct 09 09:22:42 2015 -0400
@@ -0,0 +1,76 @@
+<?xml version="1.0"?>
+<tool id="transtermhp" name="TransTermHP" version="@WRAPPER_VERSION@.0">
+  <description>finds rho-independent transcription terminators in bacterial genomes</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <command><![CDATA[
+#if $reference_genome.source == 'history':
+    ln -s $reference_genome.genome_fasta genomeref.fa &&
+#end if
+
+python $__tool_directory__/transtermhp.py \$TRANSTERM_EXPTERM_DAT
+
+#if $reference_genome.source == 'cached':
+    "${reference_genome.fasta_indexes.fields.path}"
+#elif $reference_genome.source == 'history':
+    genomeref.fa
+#end if
+
+$input_gff3
+
+> $output]]></command>
+    <inputs>
+      <conditional name="reference_genome">
+          <param name="source" type="select" label="Reference Genome">
+              <option value="cached">Locally Cached</option>
+              <option value="history">From History</option>
+          </param>
+          <when value="cached">
+            <param name="fasta_indexes" type="select" label="Source FASTA Sequence">
+                <options from_data_table="all_fasta"/>
+            </param>
+        </when>
+        <when value="history">
+            <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
+        </when>
+    </conditional>
+    <param name="input_gff3" type="data" format="gff3" label="GFF3 formatted Gene Calls"/>
+
+    <!-- Currently we do not support ANY of the command line options for
+         TransTermHP due to the following statement:
+
+            As mentioned above, if you change any of the basic scoring
+            function and search parameters and are using the version 2.0
+            confidence scheme (recommended) then you have to recompute
+            the values in the expterm.dat file. If you have python
+            installed this is easy (though perhaps time consuming).
+
+            ref: http://manpages.ubuntu.com/manpages/precise/man1/transterm.1.html
+
+        This is a TODO item that would be nice to get around to eventually
+        (perhaps when a user demands it.)
+        -->
+  </inputs>
+  <outputs>
+    <data format="gff3" name="output"/>
+  </outputs>
+  <tests>
+      <test>
+          <param name="source" value="history" />
+          <param name="genome_fasta" value="sequence.fasta" />
+          <param name="input_gff3" value="sequence.gff3" />
+          <output name="output" file="sequence.gff3.out" />
+      </test>
+  </tests>
+  <help><![CDATA[
+**What it does**
+
+Finds rho-independent transcription terminators in bacterial genomes.
+]]></help>
+    <citations>
+        <citation type="doi">doi:10.1186/gb-2007-8-2-r22</citation>
+    </citations>
+</tool>