# HG changeset patch
# User iuc
# Date 1736716935 0
# Node ID 008b08870cc05fe3be5cb3d8e0df980c772f19c7

planemo upload for repository https://github.com/bluenote-1577/fairy commit 54ed1c9745f1b74e1d0a0a8353fc47f9818708e8

diff -r 000000000000 -r 008b08870cc0 fairy_sketch.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fairy_sketch.xml	Sun Jan 12 21:22:15 2025 +0000
@@ -0,0 +1,118 @@
+<tool id="fairy_sketch" name="Fairy sketch" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>sketching of k-mers for coverage into a hashtable</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code">
+        <![CDATA[
+        
+            #import re
+
+            mkdir -p res &&
+
+            #if $input.is_select == "single":
+                #set $file = re.sub('[^\s\w\-\\.]', '_', str($reads.element_identifier))
+                #set $filename = $file + '.bcsp'
+                ln -s '$reads' '$file' &&
+            #else if $input.is_select == 'pair':
+                #set $file_1 = re.sub('[^\s\w\-\\.]', '_', str($first_pairs.element_identifier))
+                #set $file_2 = re.sub('[^\s\w\-\\.]', '_', str($second_pairs.element_identifier))
+                ## Since the tool used the first inputed file to name the output file this has to be used there to cp the right file 
+                #set $filename = $file_1 + '.paired.bcsp'
+                ln -s '$first_pairs' '$file_1' &&
+                ln -s '$second_pairs' '$file_2' &&
+            #else
+                #set $file_1 = re.sub('[^\s\w\-\\.]', '_', str($paired_collection.forward.element_identifier))
+                #set $file_2 = re.sub('[^\s\w\-\\.]', '_', str($paired_collection.reverse.element_identifier))
+                ## Since the tool used the first inputed file to name the output file this has to be used there to cp the right file 
+                #set $filename = $file_1 + '.paired.bcsp'
+                ln -s '$paired_collection.forward' '$file_1' &&
+                ln -s '$paired_collection.reverse' '$file_2' &&
+            #end if
+
+            fairy sketch
+            -t "\${GALAXY_SLOTS:-3}"
+            -c ${c}
+            -k ${k}
+            -d 'res'
+            #if $input.is_select == "single":
+                -r '$file'
+            #else
+                -1 '$file_1'
+                -2 '$file_2'
+            #end if
+            &&
+
+            cp './res/${filename}' '$output'
+
+        ]]>
+    </command>
+    <inputs>
+        <conditional name="input">
+            <param name="is_select" type="select" label="Single or paired-end reads">
+                <option value="single">Single</option>
+                <option value="pair">Paired</option>
+                <option value="paired_collection">Paired collection</option>
+            </param>
+            <when value="single">
+                <param argument="--reads" type="data" format="fastqsanger,fasta,fastq,fasta.gz,fastq.gz" label="Input single-end reads"/>
+            </when>
+            <when value="pair">
+                <param argument="--first_pairs" type="data" format="fastqsanger,fasta,fastq,fasta.gz,fastq.gz" label="Input first paired-end reads"/>
+                <param argument="--second_pairs" type="data" format="fastqsanger,fasta,fastq,fasta.gz,fastq.gz" label="Input second paired-end reads"/>
+            </when>
+            <when value="paired_collection">
+                <param name="paired_collection" format="fastqsanger,fasta,fastq,fasta.gz,fastq.gz" type="data_collection" collection_type="paired" label="Input paired collection reads"/>
+            </when>
+        </conditional>
+        <param argument="-c" type="integer" value="50" optional="true" label="Set the subsampling rate"/>
+        <param argument="-k" type="select" label="Select k-mer size">
+            <option value="31">31</option>
+            <option value="21">21</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="bcsp" label="${tool.name} on ${on_string}"/>
+    </outputs>
+    <tests>
+        <test>
+            <conditional name="input">
+                <param name="is_select" value="single"/>
+                <param name="reads" value="single_test.fasta.gz" ftype="fasta.gz"/>
+            </conditional>
+            <output name="output" file="single_test.fasta.gz.bcsp"/>
+        </test>
+        <test>
+            <conditional name="input">
+                <param name="is_select" value="pair"/>
+                <param name="first_pairs" value="test_paired_1.fq.gz" ftype="fastq.gz"/>
+                <param name="second_pairs" value="test_paired_2.fq.gz" ftype="fastq.gz"/>
+            </conditional>
+            <output name="output" file="test_paired_1.fq.gz.paired.bcsp"/>
+        </test>
+        <test>
+            <conditional name="input">
+                <param name="is_select" value="paired_collection"/>
+                <param name="paired_collection">
+                    <collection type="paired">
+                        <element name="forward" value="test_paired_1.fq.gz" ftype="fastq.gz" />
+                        <element name="reverse" value="test_paired_2.fq.gz" ftype="fastq.gz" />
+                    </collection>
+                </param>    
+            </conditional>
+            <output name="output" file="forward.paired.bcsp"/>
+        </test>
+    </tests>
+    <help>
+        <![CDATA[
+
+        This tool sketch the k-mer into a hashtable which will be needed for the fairy coverage tool to create the coverage file.
+
+        .. class:: infomark
+
+            This tool can either use single-end or paired-end reads as input in multiple file formats.
+        ]]>
+    </help>
+    <expand macro="citations"/>
+</tool>
\ No newline at end of file
diff -r 000000000000 -r 008b08870cc0 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Sun Jan 12 21:22:15 2025 +0000
@@ -0,0 +1,17 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">fairy</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <token name="@TOOL_VERSION@">0.5.7</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">24.1</token>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1101/2024.04.23.590803</citation>
+            <yield/>
+        </citations>
+    </xml>
+</macros>
\ No newline at end of file
diff -r 000000000000 -r 008b08870cc0 test-data/forward.paired.bcsp
Binary file test-data/forward.paired.bcsp has changed
diff -r 000000000000 -r 008b08870cc0 test-data/normal_test.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/normal_test.tsv	Sun Jan 12 21:22:15 2025 +0000
@@ -0,0 +1,2 @@
+contigName	contigLen	totalAvgDepth	single_test.fasta.gz	single_test.fasta.gz-var
+NZ_CP017438.1	3123040	0.05509718146076748	0.05509718146076748	0.014618167653679848
diff -r 000000000000 -r 008b08870cc0 test-data/single_test.fasta.gz
Binary file test-data/single_test.fasta.gz has changed
diff -r 000000000000 -r 008b08870cc0 test-data/single_test.fasta.gz.bcsp
Binary file test-data/single_test.fasta.gz.bcsp has changed
diff -r 000000000000 -r 008b08870cc0 test-data/test_2.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_2.tsv	Sun Jan 12 21:22:15 2025 +0000
@@ -0,0 +1,1 @@
+NZ_CP017438.1	0.05509718146076748
diff -r 000000000000 -r 008b08870cc0 test-data/test_3.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_3.tsv	Sun Jan 12 21:22:15 2025 +0000
@@ -0,0 +1,2 @@
+contigName
+NZ_CP017438.1
diff -r 000000000000 -r 008b08870cc0 test-data/test_paired_1.fq.gz
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diff -r 000000000000 -r 008b08870cc0 test-data/test_paired_1.fq.gz.paired.bcsp
Binary file test-data/test_paired_1.fq.gz.paired.bcsp has changed
diff -r 000000000000 -r 008b08870cc0 test-data/test_paired_2.fq.gz
Binary file test-data/test_paired_2.fq.gz has changed