# HG changeset patch
# User iuc
# Date 1632594465 0
# Node ID 1df9f64cddd5f000bdbfd3a0ad0c98e387df61d1
# Parent  a4994292ab595f671e3054edba446b92818e56e9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit d52e3c9c53dd358e14e65a3a083e7d5c102f8697"

diff -r a4994292ab59 -r 1df9f64cddd5 presto_macros.xml
--- a/presto_macros.xml	Wed Sep 01 08:14:30 2021 +0000
+++ b/presto_macros.xml	Sat Sep 25 18:27:45 2021 +0000
@@ -11,7 +11,8 @@
         </xrefs>
     </xml>
     <token name="@TOOL_VERSION@">0.6.2</token>
-    
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">20.05</token>
     <xml name="requirements">
         <requirements>
               <requirement type="package" version="@TOOL_VERSION@">presto</requirement>
@@ -46,7 +47,7 @@
     
     <token name="@HELP_NOTE@"><![CDATA[
 
-====
+===
 
 **Note about limitations of pRESTO tools within Galaxy:**
 
diff -r a4994292ab59 -r 1df9f64cddd5 presto_macros.xml.orig
--- a/presto_macros.xml.orig	Wed Sep 01 08:14:30 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,65 +0,0 @@
-<macros>
-    <xml name="citations">
-        <citations>
-            <citation type="doi">10.1093/bioinformatics/btu138</citation>
-            <yield />
-        </citations>
-    </xml>
-<<<<<<< HEAD
-
-    <token name="@TOOL_VERSION@">0.6.2</token>
-    
-=======
-    <xml name="bio_tools">
-        <xrefs>
-            <xref type='bio.tools'>presto</xref>
-        </xrefs>
-    </xml>
->>>>>>> 7abad681f (add tools up until P)
-    <xml name="requirements">
-        <requirements>
-              <requirement type="package" version="@TOOL_VERSION@">presto</requirement>
-        </requirements>
-    </xml>
-    
-    <xml name="presto-coord-param">
-        <param argument="--coord" type="select"  value="presto"  label="Coordinate" help="The format of the sequence identifier which defines shared coordinate information across mate pairs.">
-            <option value="illumina">Illumina</option>
-            <option value="solexa">Solexa</option>
-            <option value="sra">SRA</option>
-            <option value="454">454</option>
-            <option value="presto">pRESTO</option>
-        </param>
-    </xml>
-    
-    <xml name="presto-log-param">
-        <param name="capture_log" type="boolean" value="false" label="Generate Detailed Log" help="Generate detailed log information that can be summarized with ParseLog."/>
-    </xml>
-    
-    <xml name="presto-log-output">
-        <data name="log_out" format="txt" label="Log from ${tool.name} on ${on_string}">
-            <filter>capture_log</filter>
-        </data>
-    </xml>
-    
-    <xml name="text-regex-validator">
-        <validator type="regex" message="Value may include alphanumeric characters, underscores and spaces.">[A-Za-z0-9_ ]+</validator>
-    </xml>
-
-    <token name="@PRESTO_URL_BASE@">https://presto.readthedocs.io</token>
-    
-    <token name="@HELP_NOTE@"><![CDATA[
-
-====
-
-**Note about limitations of pRESTO tools within Galaxy:**
-
-pRESTO tools in galaxy have the following limitations vs. when run at the command line:
-
-* Inputs must be FASTQ format and cannot be FASTA format.
-* Multiple inputs files are not supported per argument (e.g. ``-1``, ``-2`` or ``-s``), i.e.
-    - Steps that take a pair of fastq inputs can only take two files, not two sets of files
-    - Steps that take a single set of fastq inputs can only take a single file
-* The ``--outdir`` and ``--outname`` options are not supported; output files are named directly
-    ]]></token>
-</macros>
diff -r a4994292ab59 -r 1df9f64cddd5 presto_pairseq.xml
--- a/presto_pairseq.xml	Wed Sep 01 08:14:30 2021 +0000
+++ b/presto_pairseq.xml	Sat Sep 25 18:27:45 2021 +0000
@@ -1,12 +1,12 @@
-<tool id="presto_pairseq" name="pRESTO PairSeq" version="@TOOL_VERSION@">
+<tool id="presto_pairseq" name="pRESTO PairSeq" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Sorts and matches sequence records with matching coordinates across files</description>
     <expand macro="bio_tools"/>
     <macros>
         <import>presto_macros.xml</import>
-    </macros>
-    
-    <expand macro="requirements"/>
-    
+	</macros>
+
+	<expand macro="requirements"/>
+
     <version_command>PairSeq.py --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
         ln -s '$r1_in' r1.fastq &&
@@ -21,6 +21,7 @@
           #if $r2_annotations
           --2f $r2_annotations
           #end if
+		  $failed
           --outdir=.
           --outname=tmp
     ]]></command>
@@ -34,14 +35,21 @@
             <expand macro="text-regex-validator"/>
         </param>
         <expand macro="presto-coord-param"/>
+        <param argument="--failed" type="boolean" checked="false" truevalue="--failed" falsevalue="" label="Failed reads fastq output" />
     </inputs>
     <outputs>
         <data name="r1_out" format="fastq" from_work_dir="tmp-1_pair-pass.fastq"/>
         <data name="r2_out" format="fastq" from_work_dir="tmp-2_pair-pass.fastq"/>
+        <!-- only give these 2 outputs if input failed_fastq=True-->
+        <data name="r1_fail_out" format="fastq" from_work_dir="tmp-1_pair-fail.fastq">
+            <filter>failed</filter>
+        </data>
+        <data name="r2_fail_out" format="fastq" from_work_dir="tmp-2_pair-fail.fastq">
+            <filter>failed</filter>
+        </data>
     </outputs>
-    
     <tests>
-        <test>
+        <test expect_num_outputs="2">
             <param name="r1_in" value="presto_pairseq_test1_r1_in.fastq"/>
             <param name="r2_in" value="presto_pairseq_test1_r2_in.fastq"/>
             <param name="r2_annotations" value="BARCODE"/>
@@ -49,8 +57,26 @@
             <output name="r1_out" file="presto_pairseq_test1_r1_out.fastq" sort="true"/>
             <output name="r2_out" file="presto_pairseq_test1_r2_out.fastq" sort="true"/>
         </test>
+        <test expect_num_outputs="4">
+            <param name="r1_in" value="presto_pairseq_test1_r1_in.fastq"/>
+            <param name="r2_in" value="presto_pairseq_test1_r2_in.fastq"/>
+            <param name="r2_annotations" value="BARCODE"/>
+            <param name="coord" value="illumina"/>
+            <param name="failed" value="true"/>
+            <output name="r1_out" file="presto_pairseq_test1_r1_out.fastq" sort="true"/>
+            <output name="r2_out" file="presto_pairseq_test1_r2_out.fastq" sort="true"/>
+            <output name="r1_fail_out">
+                <assert_contents>
+                    <has_text text="@"/>
+                </assert_contents>
+            </output>
+            <output name="r2_fail_out">
+                <assert_contents>
+                    <has_text text="@"/>
+                </assert_contents>
+            </output>
+        </test>
     </tests>
-    
     <help><![CDATA[
 Sorts and matches sequence records with matching coordinates across files.