diff chimera.ccode.xml @ 0:3eca08ae427b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chimera.ccode.xml	Fri May 19 05:14:11 2017 -0400
@@ -0,0 +1,129 @@
+<tool profile="16.07" id="mothur_chimera_ccode" name="Chimera.ccode" version="@WRAPPER_VERSION@.0">
+    <description>Find putative chimeras using ccode</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
+    <command><![CDATA[
+        @SHELL_OPTIONS@
+
+        ## create symlinks to input datasets
+        ln -s "$fasta" fasta.dat &&
+        ln -s "$alignment.template" alignment.template.dat &&
+        #if $mask.source2 == "history":
+            ln -s "$mask.input" mask.input.dat &&
+        #end if
+
+        echo 'chimera.ccode(
+            fasta=fasta.dat,
+            reference=alignment.template.dat,
+            filter=$filter,
+            #if $mask.source2 == "default":
+                mask=default,
+            #elif $mask.source2 == "history":
+                mask=mask.input.dat,
+            #end if
+            #if int($window) > 0:
+                window=$window,
+            #end if
+            #if int($numwanted) > 0:
+                numwanted=$numwanted,
+            #end if
+            processors='\${GALAXY_SLOTS:-8}'
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <param name="fasta" type="data" format="mothur.align" label="fasta - Candiate Aligned Sequences"/>
+        <conditional name="alignment">
+            <param name="source" type="select" label="Select Reference Template from" help="">
+                <option value="hist">History</option>
+                <option value="ref">Cached Reference</option>
+            </param>
+            <when value="ref">
+                <param name="template" type="select" label="reference - Select an alignment database" help="">
+                    <options from_data_table="mothur_aligndb">
+                    </options>
+                </param>
+            </when>
+            <when value="hist">
+                <param name="template" type="data" format="fasta" label="reference - Reference to align with" help=""/>
+            </when>
+        </conditional>
+        <param name="filter" type="boolean" falsevalue="False" truevalue="True" checked="false" label="filter - Apply a 50% soft vertical filter"/>
+        <conditional name="mask">
+            <param name="source2" type="select" label="Mask option">
+                <option value="">None</option>
+                <option value="default">default ecoli mask</option>
+                <option value="history">From Your History</option>
+            </param>
+            <when value="history">
+                <param name="input" type="data" format="mothur.filter" label="Mask for the reference file" help=""/>
+            </when>
+            <when value=""/>
+            <when value="default"/>
+        </conditional>
+        <param name="window" type="integer" value="0" label="window - Length of sequence you want in each window analyzed (default if &lt; 1)" help="Recommended window size is between 5 and 20% of your trimmed sequence length. Default is 10% of the sequence length."/>
+        <param name="numwanted" type="integer" value="20" label="numwanted - Number of sequences compared with each query (uses default if set to 0)"/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="out_file" format="txt" from_work_dir="fasta.*ccode.chimeras" label="${tool.name} on ${on_string}: ccode.chimeras"/>
+        <data name="out_accnos" format="mothur.accnos" from_work_dir="fasta.*ccode.accnos" label="${tool.name} on ${on_string}: ccode.accnos"/>
+        <data name="mapinfo" format="tabular" from_work_dir="*.mapinfo" label="${tool.name} on ${on_string}: mapinfo"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
+            <param name="source" value="hist"/>
+            <param name="template" value="HMP_MOCK.v35.align"/>
+            <output name="out_file" ftype="txt">
+                <assert_contents>
+                    <has_line_matching expression="^Window\tAvgQ\t\(sdQ\)\tAvgR\t\(sdR\)\tRatio\tAnova$"/>
+                </assert_contents>
+            </output>
+            <output name="out_accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.good.ccode.accnos" ftype="mothur.accnos"/>
+            <output name="mapinfo" md5="ef3353b1467fe95a24153513917e6444" ftype="tabular"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test> <!-- test with default ecoli mask -->
+            <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
+            <param name="source" value="hist"/>
+            <param name="template" value="HMP_MOCK.v35.align"/>
+            <param name="source2" value="default"/>
+            <param name="window" value="100"/>
+            <output name="out_file" ftype="txt">
+                <assert_contents>
+                    <has_line_matching expression="^Window\tAvgQ\t\(sdQ\)\tAvgR\t\(sdR\)\tRatio\tAnova$"/>
+                </assert_contents>
+            </output>
+            <output name="out_accnos" md5="47ddf86ec36aafd495aa902b3e06ffca" ftype="mothur.accnos"/>
+            <output name="mapinfo" md5="25221b1e109d9c0a939efb319e7a9896" ftype="tabular"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The chimera.ccode_ command identifies putative chimeras using the ccode approach (Chimera and Cross-Over Detection and Evaluation).  Ccode_ compares differences in distances, for each word, between query sequence and reference sequences, and reference sequences and themselves.
+
+This method was written using the algorithms described in the paper_ "Evaluating putative chimeric sequences from PCR-amplified products" by Juan M. Gonzalez, Johannes Zimmerman and Cesareo Saiz-Jimenez.
+
+The program can analyze sequences for any required word length. Generally, values of 5-20% of sequence length appear to deliver accurate results, for example, working on 16S rDNA sequences with a full-length of #1500 nt. It should be noted that the use of fragments either too long or too short might result in a reduction of sensitivity.
+
+.. _Ccode: http://www.microextreme.net/downloads.html
+.. _paper: http://bioinformatics.oxfordjournals.org/content/21/3/333.full.pdf
+.. _chimera.ccode: https://www.mothur.org/wiki/Chimera.ccode
+
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>