diff tools/protein_analysis/psortb.xml @ 18:eb6ac44d4b8e draft

Suite v0.2.8, record Promoter 2 verion + misc internal updates

--- a/tools/protein_analysis/psortb.xml	Fri Nov 21 08:19:09 2014 -0500
+++ b/tools/protein_analysis/psortb.xml	Tue Sep 01 09:56:36 2015 -0400
@@ -1,61 +1,62 @@
-<tool id="Psortb" name="psortb" version="0.0.5">
-  <description>Determines sub-cellular localisation of bacterial/archaeal protein sequences</description>
-  <!-- If job splitting is enabled, break up the query file into parts -->
-  <!-- Using 2000 chunks meaning 4 threads doing 500 each is ideal -->
-  <parallelism method="basic" split_inputs="fasta_file" split_mode="to_size" split_size="2000" merge_outputs="tabular_file"></parallelism>
-  <version_command interpreter="python">psortb.py --version</version_command>
-  <command interpreter="python">
-    psortb.py "\$GALAXY_SLOTS" "$type" "$long" "$cutoff" "$divergent" "$sequence" "$outfile"
-    ##If the environment variable isn't set, get "", and python wrapper
-    ##defaults to four threads.
-  </command>
-  <stdio>
-    <!-- Anything other than zero is an error -->
-    <exit_code range="1:" />
-    <exit_code range=":-1" />
-  </stdio>
-  <inputs>
-    <param format="fasta" name="sequence" type="data"
-           label="Input sequences for which to predict localisation (protein FASTA format)" />
-    <param name="type" type="select"
-           label="Organism type (N.B. all sequences in the above file must be of the same type)" >
-      <option value="-p">Gram positive bacteria</option>
-      <option value="-n">Gram negative bacteria</option>
-      <option value="-a">Archaea</option>
-    </param>
-    <param name="long" type="select" label="Output type">
-      <option value="terse">Short (terse, tabular with 3 columns)</option>
-      <!-- The normal output is text, not tabular - worth offering?
-      <option value="normal">Normal</option>
-      -->
-      <option value="long">Long (verbose, tabular with about 30 columns, depending on organism type)</option>
-    </param>
-    <param name="cutoff" size="10" type="float" optional="true" value=""
-           label="Sets a cutoff value for reported results (e.g. 7.5)"
-           help="Leave blank or use zero for no cutoff." />
-    <param name="divergent" size="10" type="float" optional="true" value=""
-           label="Sets a cutoff value for the multiple localization flag (e.g. 4.5)"
-           help="Leave blank or use zero for no cutoff." />
-  </inputs>
-  <outputs>
-    <data format="tabular" name="outfile" />
-  </outputs>
-  <requirements>
-    <requirement type="binary">psort</requirement>
-  </requirements>
-  <tests>
-    <test>
-      <param name="sequence" value="empty.fasta" ftype="fasta"/>
-      <param name="long" value="terse"/>
-      <output name="outfile" file="empty_psortb_terse.tabular" ftype="tabular"/>
-    </test>
-    <test>
-      <param name="sequence" value="k12_ten_proteins.fasta" ftype="fasta"/>
-      <param name="long" value="terse"/>
-      <output name="outfile" file="k12_ten_proteins_psortb_p_terse.tabular" ftype="tabular"/>
-    </test>
-  </tests>
-  <help>
+<tool id="Psortb" name="psortb" version="0.0.7">
+    <description>Determines sub-cellular localisation of bacterial/archaeal protein sequences</description>
+    <!-- If job splitting is enabled, break up the query file into parts -->
+    <!-- Using 2000 chunks meaning 4 threads doing 500 each is ideal -->
+    <parallelism method="basic" split_inputs="fasta_file" split_mode="to_size" split_size="2000" merge_outputs="tabular_file"></parallelism>
+    <requirements>
+        <requirement type="binary">psort</requirement>
+        <requirement type="package">psort</requirement>
+    </requirements>
+    <stdio>
+        <!-- Anything other than zero is an error -->
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
+    <version_command interpreter="python">psortb.py --version</version_command>
+    <command interpreter="python">
+psortb.py "\$GALAXY_SLOTS" "$type" "$long" "$cutoff" "$divergent" "$sequence" "$outfile"
+##If the environment variable isn't set, get "", and python wrapper
+##defaults to four threads.
+    </command>
+    <inputs>
+        <param format="fasta" name="sequence" type="data"
+               label="Input sequences for which to predict localisation (protein FASTA format)" />
+        <param name="type" type="select"
+               label="Organism type (N.B. all sequences in the above file must be of the same type)" >
+            <option value="-p">Gram positive bacteria</option>
+            <option value="-n">Gram negative bacteria</option>
+            <option value="-a">Archaea</option>
+        </param>
+        <param name="long" type="select" label="Output type">
+            <option value="terse">Short (terse, tabular with 3 columns)</option>
+            <!-- The normal output is text, not tabular - worth offering?
+            <option value="normal">Normal</option>
+            -->
+            <option value="long">Long (verbose, tabular with about 30 columns, depending on organism type)</option>
+        </param>
+        <param name="cutoff" size="10" type="float" optional="true" value=""
+               label="Sets a cutoff value for reported results (e.g. 7.5)"
+               help="Leave blank or use zero for no cutoff." />
+        <param name="divergent" size="10" type="float" optional="true" value=""
+               label="Sets a cutoff value for the multiple localization flag (e.g. 4.5)"
+               help="Leave blank or use zero for no cutoff." />
+    </inputs>
+    <outputs>
+        <data format="tabular" name="outfile" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="sequence" value="empty.fasta" ftype="fasta"/>
+            <param name="long" value="terse"/>
+            <output name="outfile" file="empty_psortb_terse.tabular" ftype="tabular"/>
+        </test>
+        <test>
+            <param name="sequence" value="k12_ten_proteins.fasta" ftype="fasta"/>
+            <param name="long" value="terse"/>
+            <output name="outfile" file="k12_ten_proteins_psortb_p_terse.tabular" ftype="tabular"/>
+        </test>
+    </tests>
+    <help>
 
 **What it does**
 
@@ -99,9 +100,9 @@
 
 This wrapper is available to install into other Galaxy Instances via the Galaxy
 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
+    </help>
     <citations>
         <citation type="doi">10.7717/peerj.167</citation>
         <citation type="doi">10.1093/bioinformatics/btq249</citation>
     </citations>
-  </help>
 </tool>