# HG changeset patch
# User iuc
# Date 1630483756 0
# Node ID 2a9cac0ff8ff28585642e70a8ff51bd3e73da4de
# Parent  777c874f395ac411e3ba552e68361be650177daf
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"

diff -r 777c874f395a -r 2a9cac0ff8ff presto_filterseq.xml
--- a/presto_filterseq.xml	Fri Jul 02 15:20:43 2021 +0000
+++ b/presto_filterseq.xml	Wed Sep 01 08:09:16 2021 +0000
@@ -1,6 +1,6 @@
 <tool id="presto_filterseq" name="pRESTO FilterSeq" version="@TOOL_VERSION@">
     <description>Filters and/or masks reads based on length, quality, missing bases and repeats.</description>
-    
+    <expand macro="bio_tools"/>
     <macros>
         <import>presto_macros.xml</import>
     </macros>
diff -r 777c874f395a -r 2a9cac0ff8ff presto_macros.xml
--- a/presto_macros.xml	Fri Jul 02 15:20:43 2021 +0000
+++ b/presto_macros.xml	Wed Sep 01 08:09:16 2021 +0000
@@ -5,7 +5,11 @@
             <yield />
         </citations>
     </xml>
-
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">presto</xref>
+        </xrefs>
+    </xml>
     <token name="@TOOL_VERSION@">0.6.2</token>
     
     <xml name="requirements">
diff -r 777c874f395a -r 2a9cac0ff8ff presto_macros.xml.orig
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/presto_macros.xml.orig	Wed Sep 01 08:09:16 2021 +0000
@@ -0,0 +1,65 @@
+<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>