diff stacks_clonefilter.xml @ 0:a8a0cd05d47d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
author iuc
date Sun, 21 May 2017 18:54:11 -0400
parents
children a0a51078cb61
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/stacks_clonefilter.xml	Sun May 21 18:54:11 2017 -0400
@@ -0,0 +1,148 @@
+<tool id="stacks_clonefilter" name="Stacks: clone filter" version="@WRAPPER_VERSION@.0">
+<description>Identify PCR clones</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <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
+
+
+            #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
+
+           -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_pair" type="select" label="Barcode location">
+                    <expand macro="barcode_encoding_single" />
+                </param>
+            </when>
+        </conditional>
+        <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"/>
+
+    </inputs>
+    <outputs>
+        <data format="fastqsangergz" name="clean" from_work_dir="clone_outputs/R1.fq.gz">
+            <filter>data_type['dt_select'] == 'single'</filter>
+        </data>
+
+        <data format="fastqsangergz" name="clean_fwd" from_work_dir="clone_outputs/R1.1.fq.gz">
+            <filter>data_type['dt_select'] == 'pair'</filter>
+        </data>
+        <data format="fastqsangergz" name="clean_rev" from_work_dir="clone_outputs/R2.2.fq.gz">
+            <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" />
+            </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>