diff picard_SamToFastq.xml @ 31:585027e65f3b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 70d2a66c405be58d4413753792bcadf212a4da84

--- a/picard_SamToFastq.xml	Mon Aug 22 09:56:00 2022 +0000
+++ b/picard_SamToFastq.xml	Sat Feb 25 20:33:49 2023 +0000
@@ -2,7 +2,7 @@
     <description>extract reads and qualities from SAM/BAM dataset and convert to fastq</description>
     <macros>
         <import>picard_macros.xml</import>
-        <token name="@WRAPPER_VERSION@">2</token>
+        <token name="@WRAPPER_VERSION@">3</token>
     </macros>
     <xrefs>
         <xref type="bio.tools">picard_samtofastq</xref>
@@ -107,7 +107,6 @@
     <test>
       <param name="inputFile" value="picard_SamToFastq.bam" ftype="bam"/>
       <param name="single_or_paired" value="pe_interleaved" />
-      <param name="output_per_rg" value="false"/>
       <param name="re_reverse" value="true"/>
       <param name="include_non_pf_reads" value="false"/>
       <param name="clipping_attribute" value="" />
@@ -122,7 +121,6 @@
     <test>
       <param name="inputFile" value="picard_SamToFastq.bam" ftype="bam"/>
       <param name="single_or_paired" value="pe_sep" />
-      <param name="output_per_rg" value="false"/>
       <param name="re_reverse" value="true"/>
       <param name="include_non_pf_reads" value="false"/>
       <param name="clipping_attribute" value="" />
@@ -139,7 +137,6 @@
     <test>
       <param name="inputFile" value="picard_SamToFastq_se.bam" ftype="bam"/>
       <param name="single_or_paired" value="se" />
-      <param name="output_per_rg" value="false"/>
       <param name="re_reverse" value="true"/>
       <param name="include_non_pf_reads" value="false"/>
       <param name="clipping_attribute" value="" />
@@ -164,34 +161,21 @@
 
 .. class:: warningmark
 
-**DANGER: Multiple Outputs**
-
-Generating per readgroup fastq (setting **OUTPUT_PER_RG** to True) may produce very large numbers of outputs. Know what you are doing!
-
 @dataset_collections@
 
 @description@
 
   FASTQ=File
   F=File                        Output fastq file (single-end fastq or, if paired, first end of the pair fastq).
-                                Required.  Cannot be used in conjuction with option(s) OUTPUT_PER_RG (OPRG)
+                                Required.
 
   SECOND_END_FASTQ=File
   F2=File                       Output fastq file (if paired, second end of the pair fastq).  Default value: null.
-                                Cannot be used in conjuction with option(s) OUTPUT_PER_RG (OPRG)
+                                
 
   UNPAIRED_FASTQ=File
   FU=File                       Output fastq file for unpaired reads; may only be provided in paired-fastq mode  Default
-                                value: null.  Cannot be used in conjuction with option(s) OUTPUT_PER_RG (OPRG)
-
-  OUTPUT_PER_RG=Boolean
-  OPRG=Boolean                  Output a fastq file per read group (two fastq files per read group if the group is
-                                paired).  Default value: false. Possible values: {true, false}  Cannot be used in
-                                conjuction with option(s) SECOND_END_FASTQ (F2) UNPAIRED_FASTQ (FU) FASTQ (F)
-
-  OUTPUT_DIR=File
-  ODIR=File                     Directory in which to output the fastq file(s).  Used only when OUTPUT_PER_RG is true.
-                                Default value: null.
+                                value: null.
 
   RE_REVERSE=Boolean
   RC=Boolean                    Re-reverse bases and qualities of reads with negative strand flag set before writing them