Mercurial > repos > caleb-easterly > validate_fasta_database

diff validate_fasta_database.xml @ 9:d7f67cc9a9e7 draft default tip

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planemo upload commit ea998f84bf4eb1f6f6ece4eb7fc725920f9c78c4-dirty
author caleb-easterly
date Thu, 14 Sep 2017 11:13:16 -0400
parents ba8bbfd8933e
children
line wrap: on
line diff
--- a/validate_fasta_database.xml	Mon Jul 17 16:51:38 2017 -0400
+++ b/validate_fasta_database.xml	Thu Sep 14 11:13:16 2017 -0400
@@ -1,11 +1,12 @@
-<tool id="validate_fasta_database" name="Validate FASTA Database" version="0.1.3">
+<tool id="validate_fasta_database" name="Validate FASTA Database" version="0.1.4">
     <requirements>
+        <requirement type="package" version="1.0">validate-fasta-database</requirement>
     </requirements>
     <stdio>
         <exit_code range="1" level="fatal" description="Invalid FASTA headers detected, was asked to fail"/>
     </stdio>
     <command detect_errors="exit_code"><![CDATA[
-        java -jar $__tool_directory__/validate_fasta_database-0.2.jar
+        validate-fasta-database
         '$inFasta'
         '$goodFastaOut'
         '$badFastaOut'
@@ -34,24 +35,10 @@
         <param type="integer" name="minimumLength"
                label="Minimum length for sequences to pass"
                value="0"/>
-
-
-        <!--<conditional name="checkLength">-->
-            <!--<param type="boolean" name="checkLength" label="Filter out sequences below a minimum sequenceLength?">-->
-                <!--<option value="true"></option>-->
-                <!--<option value="false"></option>-->
-            <!--</param>-->
-            <!--<when value="true">-->
-                <!--<param name="minimumLength" type="integer" value="0" label="Minimum sequenceLength that AA sequence must have"/>-->
-            <!--</when>-->
-            <!--<when value="false">-->
-            <!--</when>-->
-        <!--</conditional>-->
-
     </inputs>
     <outputs>
-        <data name="goodFastaOut" format="fasta" label="Validate FASTA: Passed Sequences"/>
-        <data name="badFastaOut" format="fasta" label="Validate FASTA: Failed Sequences"/>
+        <data name="goodFastaOut" format="fasta" label="Validate FASTA ${on_string}: passed"/>
+        <data name="badFastaOut" format="fasta" label="Validate FASTA ${on_string}: failed"/>
     </outputs>
     <tests>
         <!-- test general filtering -->