diff tools/protein_analysis/tmhmm2.xml @ 20:a19b3ded8f33 draft

v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes

--- a/tools/protein_analysis/tmhmm2.xml	Wed Feb 01 09:46:42 2017 -0500
+++ b/tools/protein_analysis/tmhmm2.xml	Thu Sep 21 11:35:20 2017 -0400
@@ -1,28 +1,23 @@
-<tool id="tmhmm2" name="TMHMM 2.0" version="0.0.14">
+<tool id="tmhmm2" name="TMHMM 2.0" version="0.0.16">
     <description>Find transmembrane domains in 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">tmhmm</requirement>
-        <requirement type="package">tmhmm</requirement>
+        <requirement type="package">tmhmm2</requirement>
     </requirements>
-    <stdio>
-        <!-- Anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-    </stdio>
-    <command interpreter="python">
-      tmhmm2.py "\$GALAXY_SLOTS" $fasta_file $tabular_file
-      ##If the environment variable isn't set, get "", and the python wrapper
-      ##defaults to four threads.
+    <version_command>
+python $__tool_directory__/tmhmm2.py --version
+    </version_command>
+    <command detect_errors="aggressive">
+python $__tool_directory__/tmhmm2.py "\$GALAXY_SLOTS" '$fasta_file' '$tabular_file'
     </command>
     <inputs>
-        <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> 
+        <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/>
         <!--
         <param name="version" type="select" display="radio" label="Model version">
             <option value="">Version 1 (old)</option>
-            <option value="" selected="True">Version 2 (default)</option>
+            <option value="" selected="true">Version 2 (default)</option>
         </param>
         -->
     </inputs>
@@ -40,7 +35,7 @@
         </test>
     </tests>
     <help>
-    
+
 **What it does**
 
 This calls the TMHMM v2.0 tool for prediction of transmembrane (TM)  helices in proteins using a hidden Markov model (HMM).
@@ -65,7 +60,7 @@
 
 One of the most common mistakes by the program is to reverse the direction of proteins with one TM segment (i.e. mixing up which end of the protein is outside and inside the membrane).
 
-Do not use the program to predict whether a non-membrane protein is cytoplasmic or not. 
+Do not use the program to predict whether a non-membrane protein is cytoplasmic or not.
 
 
 **Notes**
@@ -82,7 +77,7 @@
 In order to make it easier to use in Galaxy, the wrapper script simplifies this to remove the redundant tags, and instead adds a comment line at the top with the column names:
 
 =================================== === ===== ======= ======= ====================
-#ID                                 len	ExpAA First60 PredHel Topology 
+#ID                                 len ExpAA First60 PredHel Topology
 gi|2781234|pdb|1JLY|B               304  0.01    0.00       0 o
 gi|4959044|gb|AAD34209.1|AF069992_1 600  0.00    0.00       0 o
 gi|671626|emb|CAA85685.1|           473  0.19    0.00       0 o