diff tools/clc_assembly_cell/clc_assembler.xml @ 0:0996169ac2e8 draft

Uploaded v0.0.2, previously only on the TestToolShed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/clc_assembly_cell/clc_assembler.xml	Fri Nov 21 06:41:12 2014 -0500
@@ -0,0 +1,133 @@
+<tool id="clc_assembler" name="CLC assembler" version="0.0.2">
+    <description>Assembles reads giving a FASTA file</description>
+    <requirements>
+        <requirement type="binary">clc_assembler</requirement>
+    </requirements>
+    <version_command>\${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_assembler | grep -i version</version_command>
+    <command>\${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_assembler
+#for $rg in $read_group
+##--------------------------------------
+#if str($rg.segments.type) == "paired"
+-p $rg.segments.placement $rg.segments.dist_mode $rg.segments.min_size $rg.segments.max_size -q -i "$rg.segments.filename1" "$rg.segments.filename2"
+#end if
+##--------------------------------------
+#if str($rg.segments.type) == "interleaved"
+-p $rg.segments.placement $rg.segments.dist_mode $rg.segments.min_size $rg.segments.max_size -q "$rg.segments.filename"
+#end if
+##--------------------------------------
+#if str($rg.segments.type) == "none"
+-p no -q
+#for $f in $rg.segments.filenames
+"$f"
+#end for
+#end if
+##--------------------------------------
+#end for
+-m $min_contig_len
+-o "$out_fasta"
+--cpus \${GALAXY_SLOTS:-4}
+-v | grep -v "^Progress: "</command>
+    <stdio>
+        <!-- Assume anything other than zero is an error -->
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
+    <inputs>
+        <repeat name="read_group" title="Read Group" min="1">
+            <conditional name="segments">
+                <param name="type" type="select" label="Are these paired reads?">
+                    <option value="paired">Paired reads (as two files)</option>
+                    <option value="interleaved">Paired reads (as one interleaved file)</option>
+                    <option value="none">Unpaired reads (single or orphan reads)</option>
+                </param>
+                <when value="paired">
+                    <param name="placement" type="select" label="Pairing type (segment placing)">
+                        <option value="fb">---&gt; &lt;--- (e.g. Sanger capillary or Solexa/Illumina paired-end library)</option>
+                        <option value="bf">&lt;--- ---&gt; (e.g. Solexa/Illumina mate-pair library)</option>
+                        <option value="ff">---&gt; ---&gt;</option>
+                        <option value="bb">&lt;--- &lt;---</option>
+                    </param>
+                    <param name="dist_mode" type="select" label="How is the fragment distance measured?">
+                        <option value="ss">Start to start (e.g. Sanger capillary or Solexa/Illumina libraries)</option>
+                        <option value="se">Start to end</option>
+                        <option value="es">End to start</option>
+                        <option value="ee">End to end</option>
+                    </param>
+                    <!-- TODO - min/max validation done via the <code> tag? -->
+                    <param name="min_size" type="integer" optional="false" min="0" value=""
+                           label="Minimum size of 'good' DNA templates in the library preparation" />
+                    <param name="max_size" type="integer" optional="false" min="0" value=""
+                           label="Maximum size of 'good' DNA templates in the library preparation" />
+                    <param name="filename1" type="data" format="fastq,fasta" required="true" label="Read file one"/>
+                    <param name="filename2" type="data" format="fastq,fasta" required="true" label="Read file two"/>
+                </when>
+                <when value="interleaved">
+                    <param name="placement" type="select" label="Pairing type (segment placing)">
+                        <option value="fb">---&gt; &lt;--- (e.g. Sanger capillary or Solexa/Illumina paired-end library)</option>
+                        <option value="bf">&lt;--- ---&gt; (e.g. Solexa/Illumina mate-pair library)</option>
+                        <option value="ff">---&gt; ---&gt;</option>
+                        <option value="bb">&lt;-- &lt;--</option>
+                    </param>
+                    <param name="dist_mode" type="select" label="How is the fragment distance measured?">
+                        <option value="ss">Start to start (e.g. Sanger capillary or Solexa/Illumina libraries)</option>
+                        <option value="se">Start to end</option>
+                        <option value="es">End to start</option>
+                        <option value="ee">End to end</option>
+                    </param>
+                    <!-- TODO - min/max validation done via the <code> tag? -->
+                    <param name="min_size" type="integer" optional="false" min="0" value=""
+                           label="Minimum size of 'good' DNA templates in the library preparation" />
+                    <param name="max_size" type="integer" optional="false" min="0" value=""
+                           label="Maximum size of 'good' DNA templates in the library preparation" />
+                    <param name="filename" type="data" format="fastq,fasta" required="true" label="Interleaved read file"/>
+                </when>
+                <when value="none">
+                    <param name="filenames" type="data" format="fastq,fasta" multiple="true" required="true" label="Read file(s)"
+                           help="Multiple files allowed, for example several files of orphan reads." />
+                </when>
+            </conditional>
+        </repeat>
+        <param name="min_contig_len" type="integer" optional="false" min="1" value="200" label="Minimum contig length"/>
+        <!-- Word size? -->
+        <!-- Bubble size? -->
+        <!-- Scaffolding options? -->
+        <!-- AGP / GFF output? -->
+    </inputs>
+    <!-- min/max validation? <code file="clc_validator.py" /> -->
+    <outputs>
+        <data name="out_fasta" format="fasta" label="CLCbio assember contigs (FASTA)" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="read_group_0|segments|type" value="interleaved" />
+            <param name="read_group_0|segments|placement" value="fb" />
+            <param name="read_group_0|segments|dist_mode" value="ss" />
+            <param name="read_group_0|segments|min_size" value="1" />
+            <param name="read_group_0|segments|max_size" value="1000" />
+            <param name="read_group_0|segments|dist_mode" value="ss" />
+            <param name="read_group_0|segments|filename" value="SRR639755_mito_pairs.fastq.gz" ftype="fastqsanger" />
+            <param name="min_contig_len" value="200" />
+            <output name="out_fasta" file="SRR639755_mito_pairs.clc4_de_novo.fasta" ftype="fasta" />
+        </test>
+    </tests>
+    <help>
+
+**What it does**
+
+Runs the ``clc_assembler`` tool giving a FASTA output file. You would then
+typically map the same set of reads onto this assembly using ``cls_mapper``
+to any perform downstream analysis using the mapped reads.
+
+
+**Citation**
+
+If you use this Galaxy tool in work leading to a scientific publication please
+cite this wrapper as:
+
+Peter J.A. Cock (2013), Galaxy wrapper for the CLC Assembly Cell suite from CLCbio
+http://toolshed.g2.bx.psu.edu/view/peterjc/clc_assembly_cell
+
+This wrapper is available to install into other Galaxy Instances via the Galaxy
+Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/clc_assembly_cell
+    </help>
+</tool>