Mercurial > repos > sanbi-uwc > mothur_test

annotate tools/mothur/mantel.xml @ 0:ee4fee239fe7 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
author sanbi-uwc
date Fri, 03 Jun 2016 09:32:47 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
1 <tool profile="16.07" id="mothur_mantel" name="Mantel" version="@WRAPPER_VERSION@.0">
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
2 <description>Mantel correlation coefficient between two matrices.</description>
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
3 <macros>
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
4 <import>macros.xml</import>
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
5 </macros>
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
6 <expand macro="requirements"/>
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
7 <expand macro="version_command"/>
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
8 <command detect_errors="aggressive"><![CDATA[
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
9 echo 'mantel(
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
10 phylip1=$dist,
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
11 phylip2=$dist2,
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
12 method=$method,
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
13 iters=$iters
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
14 )'
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
15 | sed 's/ //g' ## mothur trips over whitespace
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
16 | mothur &&
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
17
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
18 ## move output files to correct destination
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
19 prefix="$dist" &&
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
20 mv mothur.*.logfile "$logfile" &&
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
21 mv \${prefix%.dat}*.mantel "$mantel"
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
22 ]]></command>
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
23 <inputs>
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
24 <param name="dist" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
25 <param name="dist2" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip2 - Distance Matrix"/>
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
26 <param name="method" type="select" optional="true" label="method - pearson, spearman, or kendall. Default: pearson">
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
27 <option value="pearson" selected="true">pearson</option>
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
28 <option value="spearman">spearman</option>
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
29 <option value="kendall">kendall</option>
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
30 </param>
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
31 <param name="iters" type="integer" value="1000" label="iters - Number of random configuration to try (default 1000)"/>
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
32 </inputs>
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
33 <outputs>
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
34 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: logfile"/>
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
35 <data name="mantel" format="tabular" label="${tool.name} on ${on_string}: mantel"/>
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
36 </outputs>
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
37 <tests>
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
38 <test>
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
39 <param name="dist" value="veg.dist"/>
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
40 <param name="dist2" value="env.dist"/>
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
41 <output name="mantel" ftype="tabular">
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
42 <assert_contents>
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
43 <has_line_matching expression="^Mantel\tpValue$"/>
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
44 </assert_contents>
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
45 </output>
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
46 <expand macro="logfile-test"/>
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
47 </test>
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
48 </tests>
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
49 <help>
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
50 <![CDATA[
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
51
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
52 @MOTHUR_OVERVIEW@
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
53
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
54 **Command Documenation**
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
55
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
56 The mantel_ command calculates the Mantel correlation coefficient between two matrices_.
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
57
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
58 .. _matrices: //www.mothur.org/wiki/Phylip-formatted_distance_matrix
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
59 .. _mantel: http://www.mothur.org/wiki/Mantel
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
60
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
61 ]]>
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
62 </help>
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
63 <expand macro="citations"/>
ee4fee239fe7 planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
sanbi-uwc
parents:
diff changeset
64 </tool>