diff tn93.xml @ 0:08f2130e39b3 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit f009487e8fec49f10396185ffd2fc4fe65bf4f29-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tn93.xml	Tue Mar 19 13:25:46 2019 -0400
@@ -0,0 +1,99 @@
+<tool id="tn93" name="TN93" version="1.0.4">
+    <description>compute distances between aligned sequences</description>
+    <requirements>
+        <requirement type="package" version="1.0.4">tn93</requirement>
+    </requirements>
+    <version_command><![CDATA[tn93 --version]]></version_command>
+    <command detect_errors="exit_code"><![CDATA[
+    tn93
+        -o '$tn93_distances'
+        #if str($options.advanced) == 'advanced':
+            -t $options.threshold
+            -a $options.ambigs
+            -g $options.fraction
+            -f csv
+            -l $options.overlap
+            #if $options.counts_in_name:
+                -d '$options.counts_in_name'
+            #end if
+        #end if
+        #if $second_fasta:
+            -s '$second_fasta'
+        #end if
+        '$input_fasta'
+        ]]></command>
+    <inputs>
+        <param name="input_fasta" type="data" format="fasta" label="Input in FASTA format" />
+        <param name="second_fasta" argument="-s" type="data" format="fasta" optional="true"
+            label="Additional input FASTA for pairwise comparisons" />
+        <conditional name="options">
+            <param label="Additional options" name="advanced" type="select">
+                <option value="defaults">Use defaults</option>
+                <option value="advanced">Specify additional parameters</option>
+            </param>
+            <when value="defaults" />
+            <when value="advanced">
+                <param name="threshold" type="float" value="0.015" label="Only report distances below this threshold" />
+                <param name="ambigs" argument="-a" type="select" label="Strategy for ambiguous nucleotides">
+                    <option value="handle">handle</option>
+                    <option value="resolve">resolve</option>
+                    <option value="average">average</option>
+                    <option value="skip">skip</option>
+                    <option value="gapmm">gapmm</option>
+                </param>
+                <param name="fraction" argument="-g" type="float" value="1.0"
+                    label="Maximum tolerated fraction of ambiguous characters" />
+                <param name="overlap" argument="-l" type="integer" value="100"
+                    label="Only count pairs that overlap by at least N bases" />
+                <param name="counts_in_name" argument="-d" type="text"
+                    optional="true" label="Sequence name component immediately preceding a copy number" />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="csv" name="tn93_distances" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_fasta" value="tn93-in1.fa" />
+            <param name="advanced" value="advanced" />
+            <param name="threshold" value="0.35" />
+            <output file="tn93-out1.csv" ftype="csv" name="tn93_distances" sort="True" />
+        </test>
+        <test>
+            <param name="input_fasta" value="tn93-in2-alpha.fa" />
+            <param name="second_fasta" value="tn93-in2-beta.fa" />
+            <param name="advanced" value="advanced" />
+            <param name="threshold" value="0.35" />
+            <output file="tn93-out2.csv" ftype="csv" name="tn93_distances" sort="True" />
+        </test>
+    </tests>
+    <help><![CDATA[
+TN93
+----
+
+Compute pairwise distances between aligned
+nucleotide sequences in sequential FASTA format using the
+[Tamura Nei 93 distance](http://www.ncbi.nlm.nih.gov/pubmed/8336541).
+
+NOTES
+-----
+
+All sequences must be aligned and have the same length. Only IUPAC characters are recognized (e.g. no ~). Sequence names can include copy number as in
+
+  >seqname:10
+
+':' can be replaced with another character using `-d`, and sequences that have no explicit copy number are assumed to be a single copy. Copy numbers
+only affect histogram and mean calculations.
+]]></help>
+    <citations>
+        <citation type="bibtex">
+            @UNPUBLISHED{spond,
+                author = "Sergei Kosakovsky Pond",
+                title = "HyPhy: Hypothesis Testing using Phylogenies",
+                year = "2000",
+                note = "http://hyphy.org/",
+                url = "http://hyphy.org/"}
+        </citation>
+    </citations>
+</tool>