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changeset 5:ff8599e52a55 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 1626a4a0313ab6363a214932e6dcd6f54f6ad6cf
author iuc
date Thu, 11 Apr 2019 03:22:40 -0400
parents 531ff1d417b6
children 5c265c4835c0
files art_solid.xml macros.xml
diffstat 2 files changed, 13 insertions(+), 20 deletions(-) [+]
line wrap: on
line diff
--- a/art_solid.xml	Fri Sep 07 10:57:50 2018 -0400
+++ b/art_solid.xml	Thu Apr 11 03:22:40 2019 -0400
@@ -63,7 +63,7 @@
         <param name="choice" type="select" label="Type of data to generate">
             <option value="single_end">Single-End</option>
             <option value="paired_end">Paired-End</option>
-            <option value="paired_end">Mate Pair</option>
+            <option value="mate_pair">Mate Pair</option>
         </param>
         <when value="single_end">
             <param name="LEN_READ" type="integer" label="Length of F3/R3 reads" value="100" />
--- a/macros.xml	Fri Sep 07 10:57:50 2018 -0400
+++ b/macros.xml	Thu Apr 11 03:22:40 2019 -0400
@@ -19,18 +19,15 @@
         </stdio>
     </xml>
     <xml name="aln">
-        <param type="boolean" label="output ALN alignment file (-a)" name="aln"
-            truevalue="-a" falsevalue="" />
+        <param name="aln" argument="-a" type="boolean" truevalue="-a" falsevalue="" label="Output ALN alignment file" />
     </xml>
     <xml name="sam">
-        <param type="boolean" label="output SAM alignment file (-s)" name="sam"
-            truevalue="-s" falsevalue="" />
+        <param name="sam" argument="-s" type="boolean" truevalue="-s" falsevalue="" label="Output SAM alignment file" />
     </xml>
 
     <xml name="rndSeed">
-        <param label="specify a fixed, random seed for the simulation"
-            help="Use -1 to request a random seed (-r)" name="rndSeed"
-            type="integer" value="-1" optional="true" />
+        <param name="rndSeed" argument="-r" type="integer" value="-1" optional="true" label="Fixed random seed for the simulation"
+            help="Use -1 to request a random seed" />
     </xml>
 
     <xml name="citation">
@@ -41,30 +38,26 @@
 
     <xml name="amplicon">
         <conditional name="amplicon">
-            <param name="use_amplicon" type="boolean" label="Run Amplicon Sequencing Simulation" truevalue="amplicon_true" falsevalue="amplicon_false" />
+            <param name="use_amplicon" type="boolean" truevalue="amplicon_true" falsevalue="amplicon_false" label="Run Amplicon Sequencing Simulation" />
             <when value="amplicon_true">
-                <param label="number of reads per amplicon (for 5'end amplicon sequencing)" name="reads_per_amplicon" type="integer" value="0"/>
+                <param name="reads_per_amplicon" type="integer" value="0" label="Number of reads per amplicon (for 5'end amplicon sequencing)" />
             </when>
-            <when value="amplicon_false">
-            </when>
+            <when value="amplicon_false" />
         </conditional>
     </xml>
 
     <xml name="amplicon_pair">
         <conditional name="amplicon">
-            <param name="use_amplicon" type="boolean" label="Run Amplicon Sequencing Simulation" truevalue="amplicon_true" falsevalue="amplicon_false" />
+            <param name="use_amplicon" type="boolean" truevalue="amplicon_true" falsevalue="amplicon_false" label="Run Amplicon Sequencing Simulation" />
             <when value="amplicon_true">
-                <param label="number of read pairs per amplicon (for two-end amplicon sequencing)" name="read_pairs_per_amplicon" type="integer" value="0"/>
+                <param name="read_pairs_per_amplicon" type="integer" value="0" label="Number of read pairs per amplicon (for two-end amplicon sequencing)" />
             </when>
-            <when value="amplicon_false">
-            </when>
+            <when value="amplicon_false" />
         </conditional>
     </xml>
 
     <xml name="frag_len_sd">
-        <param label="the average DNA fragment size"
-            name="fragment_size" type="integer" value="200" />
-        <param label="the standard deviation of the DNA fragment size"
-            name="fragment_sd" type="integer" value="0"/>
+        <param name="fragment_size" type="integer" value="200" label="Average DNA fragment size" />
+        <param name="fragment_sd" type="integer" value="0" label="Standard deviation of the DNA fragment size" />
     </xml>
 </macros>