diff stacks_clonefilter.xml @ 0:a46a0b4b297d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/stacks_clonefilter.xml	Thu Nov 29 12:28:26 2018 -0500
@@ -0,0 +1,153 @@
+<tool id="stacks2_clonefilter" name="Stacks2: clone filter" version="@WRAPPER_VERSION@">
+<description>Identify PCR clones</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_cmd"/>
+    <command><![CDATA[
+
+        #if $data_type.dt_select == "single"
+
+            #if $data_type.fname.is_of_type('fastqsanger')
+                #set $ext = ".fq"
+                #set inputype = "fastq"
+            #else
+                #set $ext = ".fq.gz"
+                #set inputype = "gzfastq"
+            #end if
+
+            ln -s '$data_type.fname' R1$ext &&
+        #else
+
+            #if $data_type.fwd.is_of_type('fastqsanger')
+                #set $ext = ".fq"
+                #set inputype = "fastq"
+            #else
+                #set $ext = ".fq.gz"
+                #set inputype = "gzfastq"
+            #end if
+
+            ln -s '$data_type.fwd' R1$ext &&
+            ln -s '$data_type.rev' R2$ext &&
+        #end if
+
+
+        mkdir clone_outputs
+
+        &&
+
+        clone_filter
+            #if $data_type.dt_select == 'single':
+                -f R1$ext
+            #else
+                -1 R1$ext
+                -2 R2$ext
+            #end if
+
+            -i $inputype
+
+            -o clone_outputs
+            $capture
+
+            #if $oligo_len_1
+                --oligo_len_1 $oligo_len_1
+                $data_type.barcode_encoding
+            #end if
+            #if $oligo_len_2
+                --oligo_len_2 $oligo_len_2
+            #end if
+            $retain_oligo
+            ## only supports fastq.gz output since the 
+            ## the program outputs empty files for fasta/fastq 
+            -y gzfastq
+
+    ]]></command>
+    <inputs>
+        <conditional name="data_type">
+            <param name="dt_select" type="select" label="Single or Paired-end">
+                <option value="single">Single</option>
+                <option value="pair">Pair</option>
+            </param>
+            <when value="single">
+                <param name="fname" type="data" format="fastqsanger,fastqsanger.gz" label="FASTQ" />
+                <param name="barcode_encoding" type="select" label="Barcode location">
+                    <expand macro="barcode_encoding_single" />
+                </param>
+
+            </when>
+            <when value="pair">
+                <param name="fwd" type="data" format="fastqsanger,fastqsanger.gz" label="Forward FASTQ" />
+                <param name="rev" type="data" format="fastqsanger,fastqsanger.gz" label="Reverse FASTQ" />
+                <param name="barcode_encoding" type="select" label="Barcode location">
+                    <expand macro="barcode_encoding_pair" />
+                </param>
+            </when>
+        </conditional>
+        <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file" />
+        <param name="oligo_len_1" optional="true" type="integer" label="length of the single-end oligo sequence in data set"/>
+        <param name="oligo_len_2" optional="true" type="integer" label="length of the paired-end oligo sequence in data set"/>
+        <param argument="--retain_oligo" type="boolean" checked="false" truevalue="--retain_oligo" falsevalue="" label="do not trim off the random oligo sequence (if oligo is inline)" />
+
+    </inputs>
+    <outputs>
+        <data format="fastqsanger.gz" name="clean" from_work_dir="clone_outputs/R1.fq.gz"  label="${tool.name} on ${on_string}">
+            <filter>data_type['dt_select'] == 'single'</filter>
+        </data>
+
+        <data format="fastqsanger.gz" name="clean_fwd" from_work_dir="clone_outputs/R1.1.fq.gz" label="${tool.name} on ${on_string} Forward reads">
+            <filter>data_type['dt_select'] == 'pair'</filter>
+        </data>
+        <data format="fastqsanger.gz" name="clean_rev" from_work_dir="clone_outputs/R2.2.fq.gz" label="${tool.name} on ${on_string} Reverse reads">
+            <filter>data_type['dt_select'] == 'pair'</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <conditional name="data_type">
+                <param name="dt_select" value="single" />
+                <param name="fname" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" />
+            </conditional>
+            <param name="oligo_len_1" value="6" />
+            <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.single.gz"/>
+        </test>
+        <test>
+            <conditional name="data_type">
+                <param name="dt_select" value="single" />
+                <param name="fname" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" />
+                <param name="barcode_encoding" value="--index_null" />
+            </conditional>
+            <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/>
+        </test>
+        <test>
+            <conditional name="data_type">
+                <param name="dt_select" value="pair" />
+                <param name="fwd" ftype="fastqsanger" value="clonefilter/R1_0001.1.fq.gz" />
+                <param name="rev" ftype="fastqsanger" value="clonefilter/R2_0001.2.fq.gz" />
+            </conditional>
+            <output name="clean_fwd" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/>
+            <output name="clean_rev" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz"/>
+        </test>
+        <test>
+            <conditional name="data_type">
+                <param name="dt_select" value="pair" />
+                <param name="fwd" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" />
+                <param name="rev" ftype="fastqsanger.gz" value="clonefilter/R2_0001.2.fq.gz" />
+            </conditional>
+            <output name="clean_fwd" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/>
+            <output name="clean_rev" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+.. class:: infomark
+
+
+The clone_filter program is designed to identify PCR clones.
+
+@STACKS_INFOS@
+]]>
+    </help>
+    <expand macro="citation" />
+</tool>