diff reago.xml @ 0:715b263db9f3 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/reago.xml	Tue Jan 26 08:17:20 2016 -0500
@@ -0,0 +1,138 @@
+<tool id="reago" name="Reago" version="0.1.0">
+    <description> to assemble rRNA</description>
+
+    <requirements>
+        <requirement type="package" version="1.1">infernal</requirement>
+        <requirement type="package" version="1.5.7">genometools</requirement>
+        <requirement type="package" version="1.1">reago</requirement>
+    </requirements>
+
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+
+    <command>
+<![CDATA[
+        #set $r1_output=$os.path.splitext($os.path.basename(str($r1_file)))[0]
+        #set $r2_output=$os.path.splitext($os.path.basename(str($r2_file)))[0]
+
+        python $__tool_directory__/format_reago_input_files.py 
+            --r1_input "$r1_file"
+            --r2_input "$r2_file"
+            --r1_output $r1_output
+            --r2_output $r2_output
+
+        &&  
+        python \${REAGO_DIR}/filter_input.py 
+            $r1_output
+            $r2_output
+            .
+            \${REAGO_DIR}/cm/ 
+            $cm_to_use
+            "\${GALAXY_SLOTS:-4}"
+
+        && 
+        python \${REAGO_DIR}/reago.py 
+            "filtered.fasta"
+            .
+            -l $read_length
+            -o $overlap
+            -t $tip_size 
+            -b $path_finding_parameter
+]]>
+    </command>
+
+    <inputs>
+        <param name="r1_file" type="data" format="fasta" label="R1 input sequence 
+            file" help=""/>
+
+        <param name="r2_file" type="data" format="fasta" label="R2 input sequence 
+            file" help=""/>
+
+        <param name="read_length" type="integer" min="1" max="1000" value="101" 
+            label="Read length" help="(-l)"/>
+
+        <param name="overlap" type="float" min="0" max="1" value="0.8" 
+            label="Overlap" help="(-o)"/>
+
+        <param name="tip_size" type="integer" min="0" max="1000" value="30" 
+            label="Tip size" help="(-t)"/>
+
+        <param name="path_finding_parameter" type="integer" min="2" max="11" 
+            value="10" label="Path finding parameter" help="(-b)"/>
+
+        <param name="cm_to_use" type="select" label="Database to use to to identify 16S reads" help="">
+            <option value="b">Bacteria only</option>
+            <option value="a">Archea only</option>
+            <option value="ab">Bacteria and archea</option>
+        </param>
+
+    </inputs>
+
+    <outputs>
+        <data format="fasta" name="full_genes" 
+            from_work_dir="full_genes.fasta"
+            label="Full genes of ${on_string} (Framebot)" />
+        <data format="fasta" name="fragments" 
+            from_work_dir="fragments.fasta"
+            label="Fragment genes of ${on_string} (Framebot)" />
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="r1_file" value="reago_sample_1.fasta"/>
+            <param name="r2_file" value="reago_sample_2.fasta"/>
+            <param name="read_length" value="101" />
+            <param name="overlap" value="0.8" />
+            <param name="error_correction" value="0.05" />
+            <param name="tip_size" value="30" />
+            <param name="path_finding_parameter" value="10"/>
+            <param name="cm_to_use" value="ab" />
+            <param name="cpu_nb" value="4" />
+
+            <output name="full_genes" file="reago_full_genes.fasta"/>
+            <output name="fragments" file="reago_fragments.fasta"/>
+        </test>
+    </tests>
+
+    <help>
+<![CDATA[
+
+**What it does**
+
+Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data.
+More information on `Github repository <https://github.com/chengyuan/reago-1.1>`_.
+
+-----
+
+**Input**
+
+Sequence files with r1 and r2 are required. 
+
+-----
+
+**Parameters**
+
+The parameters are 
+
+    - The overlap percentage
+    - The threshold for error correction
+    - The tip size
+    - The parameter for path finding
+
+-----
+
+**Output**
+
+Reago produces two output files:
+
+    - A sequence file with full genes
+    - A sequence file with fragment genes
+
+    ]]>
+    </help>
+
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btv231</citation>
+    </citations>
+</tool>
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