# HG changeset patch
# User thanhlv
# Date 1663858869 0
# Node ID b40614f1e3c72af0f138a3f311552f4427bd686f

"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"

diff -r 000000000000 -r b40614f1e3c7 polca.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/polca.xml	Thu Sep 22 15:01:09 2022 +0000
@@ -0,0 +1,47 @@
+<tool id="polca" name="polca" version="@VERSION@">
+    <description> Improving the consensus accuracy in genome assemblies</description>
+    <macros>
+        <token name="@VERSION@">4.0.9</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@VERSION@">masurca</requirement>
+    </requirements>
+    <version_command>polca --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+        #if $short_reads.sr_type == 'paired'
+            ln -s '$short_read.R1' reads_1.fastq.gz &&
+            ln -s '$short_read.R2' reads_2.fastq.gz &&
+        #else if str($short_reads.sr_type) == "collection"
+            ln -s '$short_read.input1.forward' reads_1.fastq.gz &&
+            ln -s '$short_read.input1.reverse' reads_2.fastq.gz &&
+        #end if
+        ln -s '${contigs}' contigs.fa &&
+        polca.sh -a contigs.fa
+        -r reads1.fastq.gz reads2.fastq.gz
+        -t \${GALAXY_SLOTS:-4}
+        -m 1G
+    ]]>    </command>
+
+    <inputs>
+        <param name="contigs" type="data" format="fastq,fastq.gz,fasta,fasta.gz" label="Long-read assembly"/>
+        <conditional name="short_reads">
+            <param name="sr_type" type="select" label="Input reads type or collection" help="Select 'paired end' for a single library or 'collection' for a paired end collection">
+                <option value="paired" selected="true">Paired End</option>
+                <option value="collection">Paired Collection</option>
+            </param>
+            <when value="paired">
+                <param name="R1" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Forward reads (R1)" help="The file of forward reads in FASTQ format"/>
+                <param name="R2" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Reverse reads (R2)" help="The file of reverse reads in FASTQ format"/>
+            </when>
+            <when value="collection">
+                <param name="input1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data_collection" collection_type="paired" label="Paired collection" help="See help section for an explanation of dataset collections"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="contigs" format="fasta" from_work_dir="contigs.PolcaCorrected.fa" label="${tool.name} on ${on_string} Polished assembly" />
+        <data name="report" format="txt" from_work_dir="contigs.report" label="${tool.name} on ${on_string} Polished report" />
+    </outputs>
+    <help><![CDATA[
+    ]]>    </help>
+</tool>
diff -r 000000000000 -r b40614f1e3c7 polca.xml.bk
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/polca.xml.bk	Thu Sep 22 15:01:09 2022 +0000
@@ -0,0 +1,49 @@
+<tool id="polca" name="polca" version="@VERSION@">
+    <description> Minimal but speedy quality control for nanopore reads</description>
+    <macros>
+        <token name="@VERSION@">4.0.9</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@VERSION@">masurca</requirement>
+    </requirements>
+    <version_command>polca --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+        #if $short_reads.sr_type == 'paired'
+            ln -s '$short_read.R1' reads_1.fastq.gz &&
+            ln -s '$short_read.R2' reads_2.fastq.gz &&
+        #else if str($short_reads.sr_type) == "collection"
+            ln -s '$short_read.input1.forward' reads_1.fastq.gz &&
+            ln -s '$short_read.input1.reverse' reads_2.fastq.gz &&
+        #end if
+        ln -s '${contigs}' contigs &&
+        polca.sh -a contigs.fa
+        -r reads1.fastq.gz reads2.fastq.gz
+        -t \${GALAXY_SLOTS:-4}
+        -m 1G
+        $no_fix
+    ]]>    </command>
+
+    <inputs>
+        <param name="contigs" type="data" format="fasta,fasta.gz" label="Assembly"/>
+        <conditional name="short_reads">
+            <param name="sr_type" type="select" label="Input reads type or collection" help="Select 'paired end' for a single library or 'collection' for a paired end collection">
+                <option value="paired" selected="true">Paired End</option>
+                <option value="collection">Paired Collection</option>
+            </param>
+            <when value="paired">
+                <param name="R1" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Forward reads (R1)" help="The file of forward reads in FASTQ format"/>
+                <param name="R2" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Reverse reads (R2)" help="The file of reverse reads in FASTQ format"/>
+            </when>
+            <when value="collection">
+                <param name="input1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data_collection" collection_type="paired" label="Paired collection" help="See help section for an explanation of dataset collections"/>
+            </when>
+        </conditional>
+        <param argument="no_fix" type="boolean" truevalue="-n" falsevalue="" checked="false" label="Do not fix errors when found." />
+    </inputs>
+    <outputs>
+        <data name="contigs" format="fasta" from_work_dir="contigs.PolcaCorrected.fa" label="${tool.name} on ${on_string} Polished assembly" />
+        <data name="report" format="fasta" from_work_dir="contigs.report" label="${tool.name} on ${on_string} Polished assembly" />
+    </outputs>
+    <help><![CDATA[
+    ]]>    </help>
+</tool>