# HG changeset patch
# User iuc
# Date 1576702812 18000
# Node ID 2c763fb1801000e207b4b0828ef75fefd79795cc
# Parent  518ba4a77274bfcb52606667f4d3dfea5a6ffea4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"

diff -r 518ba4a77274 -r 2c763fb18010 extract-partitions.xml
--- a/extract-partitions.xml	Fri Sep 07 10:59:19 2018 -0400
+++ b/extract-partitions.xml	Wed Dec 18 16:00:12 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="khmer_extract_partitions" name="Extract partitions" version="@WRAPPER_VERSION@.0">
+<tool id="khmer_extract_partitions" name="khmer: Extract partitions" version="@WRAPPER_VERSION@@TOOL_VERSION@">
     <description>Separate sequences that are annotated with partitions into grouped files</description>
     <macros>
         <token name="@BINARY@">extract-partitions.py</token>
@@ -22,15 +22,15 @@
     </command>
     <inputs>
         <expand macro="input_sequences_filenames" />
-        <param name="max_size" type="integer" label="Max group size" value="1000000"
-            help="No more than this many number of sequences will be stored in each output (--max-size/-X)"/>
+        <param argument="--max-size" name="max_size" type="integer" label="Max group size" value="1000000"
+            help="No more than this many number of sequences will be stored in each output"/>
         <param name="min_partition_size" type="integer" label="Min partition size" value="5"
             help="The minimum partition size worth keeping (--min-partition-size/-m)" />
         <param name="output_unassigned" type="boolean" checked="false" truevalue="--output-unassigned" falsevalue=""
             label="Output unassigned sequences" help="(--output-unassigned/-U)" />
     </inputs>
     <outputs>
-        <data name="distribution" format="txt" from_work_dir="output.dist" label="Partition size distribution from ${tool.name}" />
+        <data name="distribution" format="txt" from_work_dir="output.dist" label="${tool.name} on ${on_string}: Partition size distribution" />
         <collection name="groups-of-partitions" type="list">
             <discover_datasets pattern="__name__" directory="output" />
         </collection>
diff -r 518ba4a77274 -r 2c763fb18010 macros.xml
--- a/macros.xml	Fri Sep 07 10:59:19 2018 -0400
+++ b/macros.xml	Wed Dec 18 16:00:12 2019 -0500
@@ -1,8 +1,10 @@
 <macros>
-    <token name="@WRAPPER_VERSION@">3.0.0a1</token>
+    <token name="@WRAPPER_VERSION@">3.0.0a3</token>
+    <token name="@TOOL_VERSION@">+galaxy1</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@WRAPPER_VERSION@">khmer</requirement>
+            <yield/>
         </requirements>
     </xml>
     <xml name="version">
@@ -35,7 +37,7 @@
                 <option value="specific">Show</option>
             </param>
             <when value="simple">
-                <param name="tablesize" type="select" label="Sample Type" display="radio">
+                <param argument="" name="tablesize" type="select" label="Sample Type" display="radio">
                     <option value="1e9" selected="true">Microbial Genome</option>
                     <option value="2e9">Animal Transcriptome</option>
                     <option value="4e9">Small Animal Genome or Low-Diversity Metagenome</option>
@@ -43,15 +45,32 @@
                 </param>
             </when>
             <when value="specific">
-                <param name="ksize" type="integer" value="20" label="k-mer size" help="k-mer size to use" />
-                <param name="n_tables" type="integer" min="1" value="4" label="n_tables" help="number of tables to use" />
-                <param name="tablesize_specific" type="text" value="1000000.0"
+                <param argument="--ksize" name="ksize" type="integer" value="20" label="k-mer size" help="k-mer size to use" />
+                <param argument="--n_tables" name="n_tables" type="integer" min="1" value="4" label="n_tables" help="number of tables to use" />
+                <param argument="--max-tablesize" name="tablesize_specific" type="text" value="1000000.0"
                     label="tablesize" help="(--max-tablesize) upper bound on the tablesize to use" />
             </when>
         </conditional>
     </xml>
+    <token name="@LINK_SEQUENCES@">
+<![CDATA[
+#import re
+mkdir input/ &&
+#set gzip=""
+#for $num, $input in enumerate($inputs)
+    ln -s '${input}' 'input/$re.sub("[^\w\-_.]", "_", $input.element_identifier).$input.ext' &&
+    #if str($input).endswith(".gz"):
+        #set gzip="--gzip"
+    #end if
+#end for]]></token>
+    <token name="@USE_SEQUENCES@">
+<![CDATA[
+#for $num, $input in enumerate($inputs)
+    '../input/$re.sub("[^\w\-_.]", "_", $input.element_identifier).$input.ext'
+#end for]]></token>
+
     <xml name="input_sequences_filenames">
-        <param  name="inputs" multiple="true" type="data" format="fasta,fastq"
+        <param  name="inputs" multiple="true" type="data" format="fasta,fastq,fasta.gz,fastq.gz"
             label="Sequences in FASTA or FASTQ format"
             help="Put in order of precedence such as longest reads first." />
     </xml>
@@ -66,27 +85,26 @@
     </xml>
     <xml name="abundance-histogram-output">
         <data name="output_histogram_filename" format="txt"
-            label="${tool.name} k-mer abundance histogram. The
+            label="${tool.name} on ${on_string}: k-mer abundance histogram. The
                 columns are: (1) k-mer abundance, (2) k-mer count, (3)
                 cumulative count, (4) fraction of total distinct k-mers." />
     </xml>
-    <xml name="output_sequences">
-        <data name="output" format_source="inputs"
-            label="${tool.name} processed nucleotide sequence file">
-            <discover_datasets pattern="__designation_and_ext__" directory="output" visible="true"/>
-        </data>
+    <xml name="output_sequences" token_extension="">
+        <collection name="sequences" type="list">
+            <discover_datasets pattern="(?P&lt;name&gt;.*)\.(?P&lt;ext&gt;fast[aq](\.gz)?)\.@EXTENSION@" directory="output" />
+        </collection>
     </xml>
     <xml name="output_sequences_single">
         <data name="output" format_source="input_sequence_filename"
-            label="${tool.name} processed nucleotide sequence file" />
+            label="${tool.name} on ${on_string}: processed nucleotide sequence file" />
     </xml>
     <xml name="input_zero">
-        <param name="zero" type="boolean" truevalue="" falsevalue="--no-zero" checked="true"
-            help="Output zero count bins (--no-zero)" />
+        <param argument="--no-zero" name="zero" type="boolean" truevalue="" falsevalue="--no-zero" checked="true"
+            help="Output zero count bins" />
     </xml>
     <xml name="input_bigcount">
-        <param  name="bigcount" type="boolean" truevalue="" falsevalue="--no-bigcount"
-            checked="true" help="Count k-mers past 255 occurences (--no-bigcount)" />
+        <param  argument="--no-bigcount" name="bigcount" type="boolean" truevalue="" falsevalue="--no-bigcount"
+            checked="true" help="Count k-mers past 255 occurences" />
     </xml>
     <token name="@HELP_FOOTER@"><![CDATA[
 (from the khmer project: http://khmer.readthedocs.org/en/v2.0/ )]]></token>
diff -r 518ba4a77274 -r 2c763fb18010 test-data/test-abund-read-2.fa.gz
Binary file test-data/test-abund-read-2.fa.gz has changed