diff tools/protein_analysis/wolf_psort.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/wolf_psort.xml	Wed Feb 01 09:46:42 2017 -0500
+++ b/tools/protein_analysis/wolf_psort.xml	Thu Sep 21 11:35:20 2017 -0400
@@ -1,21 +1,16 @@
-<tool id="wolf_psort" name="WoLF PSORT" version="0.0.9">
+<tool id="wolf_psort" name="WoLF PSORT" version="0.0.11">
     <description>Eukaryote protein subcellular localization prediction</description>
     <requirements>
-        <requirement type="binary">runWolfPsortSummary</requirement>
-        <requirement type="binary">psort</requirement>
+        <requirement type="package">wolfpsort</requirement>
     </requirements>
-    <stdio>
-        <!-- Anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-    </stdio>
-    <command interpreter="python">
-      wolf_psort.py $organism "\$GALAXY_SLOTS" "$fasta_file" "$tabular_file"
-      ##If the environment variable isn't set, get "", and python wrapper
-      ##defaults to four threads.
+    <version_command>
+python $__tool_directory__/wolf_psort.py --version
+    </version_command>
+    <command detect_errors="aggressive">
+python $__tool_directory__/wolf_psort.py $organism "\$GALAXY_SLOTS" '$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="organism" type="select" display="radio" label="Organism">
             <option value="animal">Animal</option>
             <option value="plant">Plant</option>
@@ -48,7 +43,7 @@
         </test>
     </tests>
     <help>
-    
+
 **What it does**
 
 This calls the WoLF PSORT tool for prediction of eukaryote protein subcellular localization.
@@ -78,18 +73,18 @@
 E.R.   endoplasmic reticulum 0005783
 extr   extracellular         0005576, 0005618
 golg   Golgi apparatus       0005794(1)
-lyso   lysosome		     0005764
-mito   mitochondria	     0005739
-nucl   nuclear		     0005634
-pero   peroxisome	     0005777(2)
-plas   plasma membrane	     0005886
+lyso   lysosome              0005764
+mito   mitochondria          0005739
+nucl   nuclear               0005634
+pero   peroxisome            0005777(2)
+plas   plasma membrane       0005886
 vacu   vacuolar membrane     0005774(2)
 ====== ===================== =====================
 
 Numbers in parentheses, such as "0005856(2)" indicate that descendant "part_of"
 cellular components were also included, up to the specified depth (2 in this case).
 For example, all of the children and grandchildren of "GO:0005856" were
-included as "cysk". 
+included as "cysk".
 
 Additionally compound predictions like mito_nucl are also given.