diff picard_FastqToSam.xml @ 4:2589e6207cb4 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734

--- a/picard_FastqToSam.xml	Thu Jul 16 15:32:31 2015 -0400
+++ b/picard_FastqToSam.xml	Tue Oct 13 12:27:49 2015 -0400
@@ -4,6 +4,9 @@
     <import>picard_macros.xml</import>
   </macros>
   <expand macro="requirements" />
+  <stdio>
+    <exit_code range="1:" level="fatal"/>
+  </stdio>
   <command>
     @java_options@
     
@@ -83,7 +86,7 @@
         <param name="fastq2" type="data" format="fastq" label="Input fastq file for the second read of paired end data" help="FASTQ2"/>
       </when>
       <when value="pc">
-        <param name="fastq" type="data_collection" collection_type="paired" label="FASTQ paired dataset collection" help="FASTQ and FASTQ2; A collection of two datasets with forward and reverse reads. See help below on explanation of dataset collections"/>
+        <param name="fastq" type="data_collection" collection_type="paired" format="fastq" label="FASTQ paired dataset collection" help="FASTQ and FASTQ2; A collection of two datasets with forward and reverse reads. See help below on explanation of dataset collections"/>
       </when>
     </conditional>
       
@@ -93,16 +96,16 @@
       <option value="Solexa">Solexa (+66)</option>
     </param>
 
-    <param name="read_group_name" type="text" size="20" value="A" label="Read group name" help="READ_GROUP_NAME"/>
-    <param name="sample_name" type="text" size="20" value="sample-a" label="Sample name" help="SAMPLE_NAME"/>
-    <param name="library_name" type="text" size="20" optional="True" label="The library name" help="LIBRARY_NAME; Optional"/>
-    <param name="platform_unit" type="text" size="20" optional="True"  label="The platform unit (often run_barcode.lane)" help="PLATFORM_UNIT; Optional"/>
-    <param name="platform" type="text" size="20" optional="True"  label="The platform type (e.g. illumina, 454)" help="PLATFORM; Optional"/>
-    <param name="sequencing_center" type="text" size="20" optional="True"  label="The sequencing center from which the data originated" help="SEQUENCING_CENTER; Optional"/>
+    <param name="read_group_name" type="text" value="A" label="Read group name" help="READ_GROUP_NAME"/>
+    <param name="sample_name" type="text" value="sample-a" label="Sample name" help="SAMPLE_NAME"/>
+    <param name="library_name" type="text" optional="True" label="The library name" help="LIBRARY_NAME; Optional"/>
+    <param name="platform_unit" type="text" optional="True"  label="The platform unit (often run_barcode.lane)" help="PLATFORM_UNIT; Optional"/>
+    <param name="platform" type="text" optional="True"  label="The platform type (e.g. illumina, 454)" help="PLATFORM; Optional"/>
+    <param name="sequencing_center" type="text" optional="True"  label="The sequencing center from which the data originated" help="SEQUENCING_CENTER; Optional"/>
 
     <param name="predicted_insert_size" type="integer" min="0" max="100000" optional="True" label="Predicted median insert size, to insert into the read group header" help="PREDICTED_INSERT_SIZE; Optional"/>
-    <param name="comment" type="text" size="20" optional="True" label="Comment to include in the output dataset's header" help="COMMENT; Optional"/>
-    <param name="description" type="text" size="20" optional="True" label="Optional description information" help="DESCRIPTION; Optional"/>
+    <param name="comment" type="text" optional="True" label="Comment to include in the output dataset's header" help="COMMENT; Optional"/>
+    <param name="description" type="text" optional="True" label="Optional description information" help="DESCRIPTION; Optional"/>
     <param name="run_date" optional="True" type="text" label="Run date" help="RGDT; Optional; Format=YYYY-MM-DD (eg 1997-07-16)"/>
     <param name="min_q" type="integer" value="0" min="0" max="100" label="Minimum quality allowed in the input fastq" help="MIN_Q; An exception will be thrown if a quality is less than this value; default=0"/>
     <param name="max_q" type="integer" value="93" min="0" max="100" label="Minimum quality allowed in the input fastq" help="MAX_Q; An exception will be thrown if a quality is greater than this value; default=93"/>
@@ -142,10 +145,6 @@
     </test> 
   </tests>
   
-  <stdio>
-    <exit_code range="1:"  level="fatal"/>
-  </stdio>
-  
   <help>
 
 .. class:: infomark
@@ -221,6 +220,6 @@
 @more_info@
 
   </help>
+  <citations>
+  </citations>
 </tool>
-
-