# HG changeset patch
# User iuc
# Date 1632594110 0
# Node ID 56e5741103bb2345ab9344f3234fa8cd2cc8cea3
# Parent  2a9cac0ff8ff28585642e70a8ff51bd3e73da4de
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit d52e3c9c53dd358e14e65a3a083e7d5c102f8697"

diff -r 2a9cac0ff8ff -r 56e5741103bb presto_filterseq.xml
--- a/presto_filterseq.xml	Wed Sep 01 08:09:16 2021 +0000
+++ b/presto_filterseq.xml	Sat Sep 25 18:21:50 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="presto_filterseq" name="pRESTO FilterSeq" version="@TOOL_VERSION@">
+<tool id="presto_filterseq" name="pRESTO FilterSeq" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Filters and/or masks reads based on length, quality, missing bases and repeats.</description>
     <expand macro="bio_tools"/>
     <macros>
diff -r 2a9cac0ff8ff -r 56e5741103bb presto_macros.xml
--- a/presto_macros.xml	Wed Sep 01 08:09:16 2021 +0000
+++ b/presto_macros.xml	Sat Sep 25 18:21:50 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 2a9cac0ff8ff -r 56e5741103bb presto_macros.xml.orig
--- a/presto_macros.xml.orig	Wed Sep 01 08:09:16 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>