diff tools/protein_analysis/promoter2.xml @ 30:6d9d7cdf00fc 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/promoter2.xml	Wed Feb 01 09:46:14 2017 -0500
+++ b/tools/protein_analysis/promoter2.xml	Thu Sep 21 11:15:55 2017 -0400
@@ -1,25 +1,19 @@
-<tool id="promoter2" name="Promoter 2.0" version="0.0.10">
+<tool id="promoter2" name="Promoter 2.0" version="0.0.12">
     <description>Find eukaryotic PolII promoters in DNA sequences</description>
     <!-- If job splitting is enabled, break up the query file into parts -->
     <!-- Using 2000 per chunk so 4 threads each doing 500 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">promoter</requirement>
         <requirement type="package">promoter</requirement>
     </requirements>
-    <stdio>
-        <!-- Anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-    </stdio>
-    <version_command interpreter="python">promoter2.py --version</version_command>
-    <command interpreter="python">
-        promoter2.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__/promoter2.py --version
+    </version_command>
+    <command detect_errors="aggressive">
+python $__tool_directory__/promoter2.py "\$GALAXY_SLOTS" '$fasta_file' '$tabular_file'
     </command>
     <inputs>
-        <param name="fasta_file" type="data" format="fasta" label="FASTA file of DNA sequences"/> 
+        <param name="fasta_file" type="data" format="fasta" label="FASTA file of DNA sequences"/>
     </inputs>
     <outputs>
         <data name="tabular_file" format="tabular" label="Promoter2 on ${fasta_file.name}" />
@@ -35,7 +29,7 @@
         </test>
     </tests>
     <help>
-    
+
 **What it does**
 
 This calls the Promoter 2.0 tool for prediction of eukaryotic PolII promoter sequences using a Neural Network (NN) model.
@@ -59,7 +53,7 @@
 below 0.5 ignored
 0.5 - 0.8 Marginal prediction
 0.8 - 1.0 Medium likely prediction
-above 1.0 Highly likely prediction 
+above 1.0 Highly likely prediction
 ========= ========================
 
 Internally the input FASTA file is divided into parts (to allow multiple processors to be used), and the raw output is reformatted into this tabular layout suitable for downstream analysis within Galaxy.