diff srst2v2.xml @ 3:a98ed567ea48 draft

planemo upload

--- a/srst2v2.xml	Sat Dec 02 13:52:16 2017 -0500
+++ b/srst2v2.xml	Sat Dec 02 21:23:44 2017 -0500
@@ -63,9 +63,9 @@
       #else
           --other "'-p \${GALAXY_SLOTS:-1}'"
       #end if
-      ;
+
       #if $job_type.job == "mlst" 
-        python $__tool_directory__/scoreProfiles.py $job_type.mlst_definitions $job_type.profile_cov $job_type.profile_max_mismatch > srst2.pscores
+        ; python $__tool_directory__/scoreProfiles.py --mlst_definitions $job_type.mlst_definitions --profile_cov $job_type.profile_cov --profile_max_mismatch $job_type.profile_max_mismatch --output srst2.pscores
       #end if
 
     ]]></command>
@@ -93,9 +93,9 @@
           <param type="data" name="mlst_db" label="Fasta file of MLST alleles" format="fasta" />
           <param type="data" name="mlst_definitions" label="ST definitions for MLST scheme" format="tabular" />
           <param type="text" name="mlstdelim" value="_" format="txt" label="Character(s) separating gene name from allele number in MLST database (default &apos;_&apos;)" />
-          <param type="integer" name="mlst_max_mismatch" value="10" format="txt" label="Maximum number of mismatches per read (default 10)" />
-          <param type="float" name="profile_max_mismatch" value="1" format="txt" label="Mean mismatches for reporting profile" />
-          <param type="float" name="profile_cov" value="98" format="txt" label="Mean % Coverage for reporting profile)" />
+          <param type="integer" name="mlst_max_mismatch" value="10" format="txt" label="Maximum number of mismatches per read" />
+          <param type="float" name="profile_max_mismatch" value="1" format="txt" label="Maximum number of mismatches for reporting ST profile" />
+          <param type="float" name="profile_cov" value="98" format="txt" label="Minimum mean % coverage for reporting ST profile" />
    
         </when>
         <when value="gene">
@@ -131,9 +131,19 @@
     </inputs>
 
     <outputs>
-      <data format="tabular" type="text" label="Allele Scores" name="scores" from_work_dir="*.scores"/>
-      <data format="tabular" type="text" label="Profile Scores" name="pscores" from_work_dir="*.pscores"/>
-      <data format="tabular" type="text" label="Predicted Alleles" name="alleles" from_work_dir="*results.txt"/>
+      <data format="tabular" label="SRST2 Results" name="results" from_work_dir="*.txt"/>
+      <data format="tabular" label="SRST2 Allele Scores" name="scores" from_work_dir="*.scores">
+        <filter>job_type['job'] == "mlst"</filter>
+      </data>  
+      <data format="tabular" label="SRST2 Profile Scores" name="pscores" from_work_dir="*.pscores">
+        <filter> job_type['job'] == "mlst"</filter>
+      </data>  
+      <data format="tabular" label="SRST2 Predicted Alleles" name="alleles" from_work_dir="*results.txt">
+        <filter> job_type['job'] == "mlst"</filter>
+      </data>  
+      <data format="tabular" label="SRST2 Gene Scores" name="gscores" from_work_dir="*.scores">
+        <filter>job_type['job'] == "gene"</filter>
+      </data>  
     </outputs>
 
     <help><![CDATA[