Mercurial > repos > iuc > metaphlan

annotate metaphlan.xml @ 5:6dee4abadccb draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6
author iuc
date Sat, 03 Dec 2022 10:43:21 +0000
parents ff8f55893e7d
children 2131d7dca455
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1 <tool id="metaphlan" name="MetaPhlAn" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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diff changeset
2 <description>to profile the composition of microbial communities</description>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
3 <macros>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
4 <import>macros.xml</import>
1
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
5 <xml name="tax_lev">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
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6 <conditional name="tax_lev">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
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7 <param argument="--tax_lev" type="select" label="Taxonomic level for the relative abundance output">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
8 <option value="a" selected="true">All taxonomic levels</option>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
9 <option value="k">Kingdoms only</option>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
10 <option value="p">Phyla only</option>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
11 <option value="c">Classes only</option>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
12 <option value="o">Orders only</option>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
13 <option value="f">Families only</option>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
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14 <option value="g">Genera only</option>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
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15 <option value="s">Species only</option>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
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16 </param>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
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17 <when value="a">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
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18 <param name="split_levels" type='boolean' checked="false" truevalue='true' falsevalue='false'
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
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19 label="Generate a report for each taxonomic level?" help="It will be in addition to the default output"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
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20 </when>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
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21 <when value="k"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
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22 <when value="p"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
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23 <when value="c"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
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24 <when value="o"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
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25 <when value="f"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
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26 <when value="g"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
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27 <when value="s"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
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28 </conditional>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
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29 </xml>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
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30 <token name="@FILE_FORMATS@">fastq,fastq.gz,fastq.bz2,fasta,fasta.gz,fasta.bz2</token>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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31 </macros>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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32 <expand macro="edam_ontology"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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33 <expand macro="requirements"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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34 <version_command>metaphlan -v</version_command>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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35 <command detect_errors="aggressive"><![CDATA[
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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36 #if $inputs.in.selector == "raw"
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
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37 #if $inputs.in.raw_in.selector == "single"
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
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38 #set full_ext=$inputs.in.raw_in.in.datatype.file_ext
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
39 #if $full_ext.endswith("gz")
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
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40 #set $file_path="in"
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
41 zcat '$inputs.in.raw_in.in' > '$file_path'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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42 &&
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
43 #else if $full_ext.endswith("bz2")
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
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44 #set $file_path="in"
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
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45 bzcat '$inputs.in.raw_in.in' > '$file_path'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
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46 &&
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
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47 #else
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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48 #set $file_path=$inputs.in.raw_in.in
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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49 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
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50 #else if $inputs.in.raw_in.selector == "multiple"
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
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51 #set full_ext=$inputs.in.raw_in.in[0].datatype.file_ext
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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52 #set file_path=""
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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53 #set sep=""
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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54 #for $i, $f in enumerate($inputs.in.raw_in.in)
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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55 #if $f.datatype.file_ext != $full_ext
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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56 echo "Different datatypes for input files"
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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57 &&
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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58 exit 1
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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59 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
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60 #if $full_ext.endswith("gz")
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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61 #set fp="input_%s" % ($i)
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
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62 zcat '$f' > '$fp'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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63 &&
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
64 #else if $full_ext.endswith("bz2")
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
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65 #set fp="input_%s" % ($i)
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
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66 bzcat '$f' > '$fp'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
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67 &&
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
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68 #else
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
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69 #set fp=$f
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
70 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
71 #set $file_path+="%s%s" % ($sep, $fp)
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
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72 #set $sep=","
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
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73 #end for
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
74 #else if $inputs.in.raw_in.selector == "paired"
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
75 #set full_ext=$inputs.in.raw_in.in_f.datatype.file_ext
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
76 #if $full_ext != $inputs.in.raw_in.in_r.datatype.file_ext
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
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77 echo "Different datatypes for input paired-end files"
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
78 &&
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
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79 exit 1
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
80 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
81 #if $full_ext.endswith("gz")
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
82 zcat '$inputs.in.raw_in.in_f' > 'in_f'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
83 &&
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
84 zcat '$inputs.in.raw_in.in_r' > 'in_r'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
85 &&
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
86 #set file_path="in_f,in_r"
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
87 #else if $full_ext.endswith("bz2")
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
88 bzcat '$inputs.in.raw_in.in_f' > 'in_f'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
89 &&
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
90 bzcat '$inputs.in.raw_in.in_r' > 'in_r'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
91 &&
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
92 #set file_path="in_f,in_r"
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
93 #else
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
94 #set file_path="%s,%s" % ($inputs.in.raw_in.in_f,$inputs.in.raw_in.in_r)
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
95 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
96 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
97
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
98 #if $full_ext.startswith("fastq")
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
99 #set ext='fastq'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
100 #else if $full_ext.startswith("fasta") and $full_ext.endswith(("gz","bz2"))
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
101 #set ext='fasta'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
102 #else
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
103 #set ext=$full_ext
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
104 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
105 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
106
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
107 #if $inputs.db.db_selector == "history"
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
108 mkdir 'ref_db'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
109 &&
5
6dee4abadccb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6
iuc
parents: 3
diff changeset
110 bowtie2-build --large-index '$inputs.db.bowtie2db' 'ref_db/custom_db'
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
111 &&
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
112 python '$__tool_directory__/customizemetadata.py'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
113 transform_json_to_pkl
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
114 --json '$inputs.db.mpa_pkl'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
115 --pkl 'ref_db/custom_db.pkl'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
116 &&
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
117 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
118
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
119 metaphlan
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
120 #if $inputs.in.selector == "raw"
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
121 '$file_path'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
122 --input_type '$ext'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
123 --read_min_len $inputs.in.read_min_len
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
124 --bt2_ps '$inputs.in.mapping.bt2_ps'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
125 --min_mapq_val $inputs.in.mapping.min_mapq_val
5
6dee4abadccb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6
iuc
parents: 3
diff changeset
126 #if $ext == "sam"
6dee4abadccb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6
iuc
parents: 3
diff changeset
127 --nreads \$(cat '$file_path' | grep -c -v '^@')
6dee4abadccb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6
iuc
parents: 3
diff changeset
128 #end if
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
129 #else
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
130 '$inputs.in.in'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
131 --input_type '$inputs.in.selector'
5
6dee4abadccb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6
iuc
parents: 3
diff changeset
132 #if $inputs.in.selector == "sam"
6dee4abadccb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6
iuc
parents: 3
diff changeset
133 --nreads \$(cat '$inputs.in.in' | grep -c -v '^@')
6dee4abadccb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6
iuc
parents: 3
diff changeset
134 #end if
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
135 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
136 #if $inputs.db.db_selector == "cached"
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
137 --bowtie2db '$inputs.db.cached_db.fields.path'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
138 --index '$inputs.db.cached_db.fields.dbkey'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
139 #else
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
140 --bowtie2db 'ref_db/'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
141 --index 'custom_db'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
142 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
143 -t '$analysis.analysis_type.t'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
144 #if $analysis.analysis_type.t == "rel_ab" or $analysis.analysis_type.t == "rel_ab_w_read_stats"
1
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
145 --tax_lev '$analysis.analysis_type.tax_lev.tax_lev'
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
146 #else if $analysis.analysis_type.t == "clade_specific_strain_tracker"
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
147 --clade '$analysis.analysis_type.clade'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
148 #if str($analysis.analysis_type.min_ab) != ''
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
149 --min_ab $analysis.analysis_type.min_ab
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
150 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
151 #else if $analysis.analysis_type.t == "marker_ab_table" and str($analysis.analysis_type.nreads) != ''
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
152 --nreads $$analysis.analysis_type.nreads
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
153 #else if $analysis.analysis_type.t == "marker_pres_table" and str($analysis.analysis_type.pres_th) != ''
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
154 --pres_th $analysis.analysis_type.pres_th
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
155 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
156 --min_cu_len $analysis.min_cu_len
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
157 #if str($analysis.min_alignment_len) != ''
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
158 --min_alignment_len $analysis.min_alignment_len
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
159 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
160 #if 'add_viruses' in $analysis.organism_profiling
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
161 --add_viruses
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
162 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
163 #if 'ignore_eukaryotes' in $analysis.organism_profiling
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
164 --ignore_eukaryotes
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
165 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
166 #if 'ignore_bacteria' in $analysis.organism_profiling
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
167 --ignore_bacteria
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
168 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
169 #if 'ignore_archaea' in $analysis.organism_profiling
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
170 --ignore_archaea
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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171 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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diff changeset
172 --stat_q $analysis.stat_q
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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parents:
diff changeset
173 --perc_nonzero $analysis.perc_nonzero
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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diff changeset
174 #if $analysis.ignore_markers
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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175 --ignore_markers '$analysis.ignore_markers'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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176 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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177 $analysis.avoid_disqm
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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178 --sample_id_key '$out.sample_id_key'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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179 --sample_id '$out.sample_id'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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180 $out.use_group_representative
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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181 $out.legacy_output
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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182 $out.CAMI_format_output
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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183 $out.unknown_estimation
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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184 -o '$output_file'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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185 --bowtie2out 'bowtie2out'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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186 -s '$sam_output_file'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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187 --biom '$biom_output_file'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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188 --nproc \${GALAXY_SLOTS:-4}
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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189
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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diff changeset
190 #if $inputs.in.selector == "raw"
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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191 &&
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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192 mv 'bowtie2out' '$bowtie2out'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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193 #end if
1
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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parents: 0
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194
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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195 #if $analysis.analysis_type.tax_lev.tax_lev == 'a' and $analysis.analysis_type.tax_lev.split_levels
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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196 &&
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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parents: 0
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197 mkdir 'split_levels'
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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parents: 0
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198 &&
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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199 python '$__tool_directory__/formatoutput.py'
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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200 split_levels
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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diff changeset
201 --metaphlan_output '$output_file'
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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202 --outdir 'split_levels'
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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203 $out.legacy_output
2
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
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204
1
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205 #end if
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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parents: 0
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206
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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diff changeset
207 #if $out.krona_output
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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208 &&
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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209 python '$__tool_directory__/formatoutput.py'
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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210 format_for_krona
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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211 --metaphlan_output '$output_file'
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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212 --krona_output '$krona_output_file'
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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213 #end if
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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diff changeset
214 ]]></command>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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215 <inputs>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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216 <section name="inputs" title="Inputs" expanded="true">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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217 <conditional name="in">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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218 <param name="selector" type="select" label="Input(s)">
2
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219 <option value="raw" selected="true">Fasta/FastQ file(s) with microbiota reads</option>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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220 <option value="sam">Externally BowTie2-mapped SAM file</option>
2
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
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221 <option value="bowtie2out">Intermediary mapping file of the microbiota generated by a previous MetaPhlAn run</option>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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222 </param>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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223 <when value="raw">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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224 <conditional name="raw_in">
2
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
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225 <param name="selector" type="select" label="Fasta/FastQ file(s) with microbiota reads">
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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226 <option value="single" selected="true">One single-end file</option>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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227 <option value="multiple">Multiple single-end files</option>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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228 <option value="paired">Paired-end files</option>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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229 </param>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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230 <when value="single">
2
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
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231 <param name="in" type="data" format="@FILE_FORMATS@" label="Single-end Fasta/FastQ file with microbiota reads"/>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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232 </when>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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233 <when value="multiple">
2
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
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234 <param name="in" type="data" format="@FILE_FORMATS@" multiple="true" label="Single-end Fasta/FastQ files with microbiota reads"/>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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235 </when>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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236 <when value="paired">
2
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
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237 <param name="in_f" type="data" format="@FILE_FORMATS@" label="Forward paired-end Fasta/FastQ file with microbiota reads"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
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238 <param name="in_r" type="data" format="@FILE_FORMATS@" label="Reverse paired-end Fasta/FastQ file with microbiota reads"/>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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239 </when>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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240 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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241 <param argument="--read_min_len" type="integer" value="70" label="Minimum length of the reads to be considered when parsing the input file"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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242 <section name="mapping" title="Mapping" expanded="true">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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243 <param argument="--bt2_ps" type="select" label="Presets options for BowTie2" help="Applied only with FASTA files">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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244 <option value="sensitive">Sensitive</option>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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245 <option value="very-sensitive" selected="true">Very sensitive</option>
3
ff8f55893e7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit edceb1050e9e312ef8b1201cee35992720667b6a"
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246 <option value="sensitive-local">Sensitive local</option>
ff8f55893e7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit edceb1050e9e312ef8b1201cee35992720667b6a"
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247 <option value="very-sensitive-local">Very sensitive local</option>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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248 </param>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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249 <param argument="--min_mapq_val" type="integer" value="5" label="Minimum mapping quality value (MAPQ)"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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250 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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251 </when>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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252 <when value="sam">
2
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253 <param name="in" type="data" format="sam" label="Externally BowTie2-mapped SAM file" help="BowTie2 needs to be used first to map microbiota reads"/>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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254 </when>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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255 <when value="bowtie2out">
2
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256 <param name="in" type="data" format="tabular" label="Intermediary mapping file of the microbiota generated by a previous MetaPhlAn run"
0
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257 help="File needs to be generated with MetaPhlAn versions >3.0"/>
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258 </when>
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259 </conditional>
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260 <conditional name="db">
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261 <param name="db_selector" type="select" label="Database with clade-specific marker genes">
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262 <option value="cached" selected="true">Locally cached</option>
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263 <option value="history">From history</option>
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264 </param>
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265 <when value="cached">
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266 <param name="cached_db" label="Cached database with clade-specific marker genes" type="select">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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267 <options from_data_table="metaphlan_database">
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268 <validator message="No MetaPhlAn database is available" type="no_options" />
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269 </options>
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270 </param>
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271 </when>
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272 <when value="history">
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273 <param argument="--bowtie2db" type="data" format="fasta" label="Database with clade-specific marker genes from history"/>
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274 <param argument="--mpa_pkl" type="data" format="json" label="Metadata associate to the database with clade-specific marker genes from history"/>
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275 </when>
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276 </conditional>
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277 </section>
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278 <section name="analysis" title="Analysis" expanded="true">
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279 <conditional name="analysis_type">
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280 <param argument="-t" type="select" label="Type of analysis to perform">
2
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281 <option value="rel_ab" selected="true">rel_ab: Profiling a microbiota in terms of relative abundances</option>
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282 <option value="rel_ab_w_read_stats">rel_ab_w_read_stats: Profiling a microbiota in terms of relative abundances and estimate the number of reads comming from each clade</option>
0
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283 <option value="reads_map">reads_map: Mapping from reads to clades (only reads hitting a marker)</option>
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284 <option value="clade_profiles">clade_profiles: Normalized marker counts for clades with at least a non-null marker</option>
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285 <option value="clade_specific_strain_tracker">clade_specific_strain_tracker: List of markers present for a specific clade and all its subclades</option>
2
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286 <option value="marker_ab_table">marker_ab_table: Normalized marker counts (only when > 0.0 and normalized by microbiota size if number of reads is specified)</option>
0
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287 <option value="marker_counts">marker_counts: Non-normalized marker counts (use with extreme caution)</option>
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288 <option value="marker_pres_table">marker_pres_table: List of markers present in the sample (threshold at 1.0 if not differently specified with --pres_th</option>
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289 </param>
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290 <when value="rel_ab">
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291 <expand macro="tax_lev"/>
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292 </when>
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293 <when value="rel_ab_w_read_stats">
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294 <expand macro="tax_lev"/>
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295 </when>
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296 <when value="reads_map"/>
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297 <when value="clade_profiles"/>
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298 <when value="clade_specific_strain_tracker">
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299 <param argument="--clade" type="text" value="" label="Clade for which to extract list of markers present"
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300 help="Markers are also extracted for subclades" />
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301 <param argument="--min_ab" type="float" optional="true" label="The minimum percentage abundance for the clade"/>
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302 </when>
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303 <when value="marker_ab_table">
2
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304 <param argument="--nreads" type="integer" optional="true" label="Total number of reads in the original microbiota"
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305 help="It is used for normalizing the length-normalized counts with the microbiota size as well. No normalization applied if the value is not specified"/>
0
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306 </when>
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307 <when value="marker_counts"/>
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308 <when value="marker_pres_table">
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309 <param argument="--pres_th" type="integer" optional="true" label="Threshold for calling a marker present"/>
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310 </when>
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311 </conditional>
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312 <param argument="--min_cu_len" type="integer" value="2000"
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313 label="Minimum total nucleotide length for the markers in a clade for estimating the abundance without considering sub-clade abundances"/>
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314 <param argument="--min_alignment_len" type="integer" optional="true"
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315 label="Sam records for aligned reads with the longest subalignment length smaller than this threshold will be discarded."/>
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316 <param name="organism_profiling" type="select" multiple="true" optional="true" label="Organisms to profile">
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317 <option value="add_viruses" selected="true">Profile viral organisms (add_viruses)</option>
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318 <option value="ignore_eukaryotes">Ignore eukaryotic organisms (ignore_eukaryotes)</option>
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319 <option value="ignore_bacteria">Ignore bacteria organisms (ignore_bacteria)</option>
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320 <option value="ignore_archaea">Ignore archea organisms (ignore_archaea)</option>
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321 </param>
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322 <param argument="--stat" type="select" label="Statistical approach for converting marker abundances into clade abundances">
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323 <option value="avg_g">avg_g: Clade global (i.e. normalizing all markers together) average (avg_g)</option>
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324 <option value="avg_l">avg_l: Average of length-normalized marker counts</option>
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325 <option value="tavg_g" selected="true">tavg_g: Truncated clade global average at --stat_q quantile</option>
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326 <option value="tavg_l">tavg_l: Truncated average of length-normalized marker counts (at --stat_q)</option>
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327 <option value="wavg_g">wavg_g: Winsorized clade global average (at --stat_q)</option>
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328 <option value="wavg_l">wavg_l: Winsorized average of length-normalized marker counts (at --stat_q)</option>
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329 <option value="med">med: Median of length-normalized marker counts</option>
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330 </param>
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331 <param argument="--stat_q" type="float" value="0.2" label="Quantile value for the robust average"/>
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332 <param argument="--perc_nonzero" type="float" value="0.33" label="Percentage of markers with a non zero relative abundance for misidentify a species"/>
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333 <param argument="--ignore_markers" type="data" format="txt,tabular" optional="true" label="File containing a list of markers to ignore" help="One marker per line"/>
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334 <param argument="--avoid_disqm" type='boolean' checked="true" truevalue='--avoid_disqm' falsevalue=''
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335 label="Deactivate the procedure of disambiguating the quasi-markers based on the marker abundance pattern found in the sample?"
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336 help="It is generally recommended to keep the disambiguation procedure in order to minimize false positives"/>
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337 </section>
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338 <section name="out" title="Outputs" expanded="true">
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339 <param argument="--sample_id_key" type="text" value="SampleID" label="Sample ID key for this analysis"/>
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340 <param argument="--sample_id" type="text" value="Metaphlan_Analysis" label="Sample ID for this analysis"/>
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341 <param argument="--use_group_representative" type='boolean' checked="false" truevalue='--use_group_representative' falsevalue=''
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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342 label="Use a species as representative for species groups?"/>
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343 <param argument="--legacy-output" type='boolean' checked="false" truevalue='--legacy-output' falsevalue=''
0
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344 label="Old MetaPhlAn2 two columns output?"/>
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345 <param argument="--CAMI_format_output" type='boolean' checked="false" truevalue='--CAMI_format_output' falsevalue=''
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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346 label="Report the profiling using the CAMI output format?"/>
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347 <param argument="--unknown_estimation" type='boolean' checked="false" truevalue='--unknown_estimation' falsevalue=''
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348 label="Scale relative abundances to the number of reads mapping to known clades in order to estimate unknowness?"/>
1
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349 <param name="krona_output" type='boolean' checked="false" truevalue='true' falsevalue='false' label="Output for Krona?"/>
0
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350 </section>
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351 </inputs>
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352 <outputs>
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353 <data name="output_file" format="tabular" label="${tool.name} on ${on_string}: Predicted taxon relative abundances" />
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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354 <data name="bowtie2out" format="tabular" label="${tool.name} on ${on_string}: Bowtie2 output">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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355 <filter>inputs['in']['selector'] == "raw"</filter>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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356 </data>
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357 <data name="sam_output_file" format="sam" label="${tool.name} on ${on_string}: SAM file">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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358 <filter>inputs['in']['selector'] == "raw"</filter>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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359 </data>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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360 <data name="biom_output_file" format="biom1" label="${tool.name} on ${on_string}: BIOM file" />
1
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361 <collection name="levels" type="list" label="${tool.name} on ${on_string}: Predicted taxon relative abundances at each taxonomic levels" >
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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362 <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="split_levels/" format="tabular"/>
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363 <filter>analysis['analysis_type']['tax_lev']['tax_lev'] == "a" and analysis['analysis_type']['tax_lev']['split_levels']</filter>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
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364 </collection>
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365 <data name="krona_output_file" format="tabular" label="${tool.name} on ${on_string}: Predicted taxon relative abundances for Krona">
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366 <filter>out['krona_output']</filter>
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367 </data>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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368 </outputs>
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369 <tests>
1
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370 <test expect_num_outputs="6">
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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371 <section name="inputs">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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372 <conditional name="in">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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373 <param name="selector" value="raw"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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374 <conditional name="raw_in">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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375 <!-- Single GZ file -->
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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376 <param name="selector" value="single"/>
2
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377 <param name="in" value="no_taxon_input.fasta"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
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378 </conditional>
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379 <param name="read_min_len" value="70"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
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380 <section name="mapping">
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381 <param name="bt2_ps" value="sensitive"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
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382 <param name="min_mapq_val" value="5"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
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383 </section>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
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384 </conditional>
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385 <conditional name="db">
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386 <!-- Cached db -->
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
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387 <param name="db_selector" value="cached"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
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388 <param name="cached_db" value="test-db-20210409"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
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389 </conditional>
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390 </section>
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391 <section name="analysis">
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392 <conditional name="analysis_type">
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393 <param name="t" value="rel_ab"/>
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394 <conditional name="tax_lev">
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395 <param name="tax_lev" value="a"/>
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396 <param name="split_levels" value="true"/>
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397 </conditional>
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398 </conditional>
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399 <param name="min_cu_len" value="2000"/>
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400 <param name="organism_profiling" value="add_viruses"/>
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401 <param name="stat" value="avg_g"/>
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402 <param name="stat_q" value="0.2"/>
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403 <param name="perc_nonzero" value="0.33"/>
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404 <param name="avoid_disqm" value="true"/>
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405 </section>
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406 <section name="out">
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407 <param name="sample_id_key" value="SampleID"/>
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408 <param name="sample_id" value="Metaphlan_Analysis"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
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409 <param name="use_group_representative" value="false"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
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410 <param name="legacy_output" value="false"/>
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411 <param name="CAMI_format_output" value="false"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
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412 <param name="unknown_estimation" value="false"/>
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413 <param name="krona_output" value="true"/>
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414 </section>
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415 <output name="output_file" ftype="tabular">
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416 <assert_contents>
5
6dee4abadccb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6
iuc
parents: 3
diff changeset
417 <has_text text="UNCLASSIFIED"/>
2
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
418 </assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
419 </output>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
420 <output name="bowtie2out" ftype="tabular">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
421 <assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
422 <not_has_text text="HWI-EAS109_102883399:3:104:7342:14360/1"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
423 <has_n_lines n="2"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
424 </assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
425 </output>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
426 <output name="sam_output_file" ftype="sam">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
427 <assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
428 <has_text text="SN:13076__A0A2I1PE66__CYJ72_10760"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
429 </assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
430 </output>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
431 <output name="biom_output_file" ftype="biom1">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
432 <assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
433 <not_has_text text="k__Bacteria"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
434 <not_has_text text="p__Actinobacteria"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
435 </assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
436 </output>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
437 <output_collection name="levels" type="list" >
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
438 <element name="all" ftype="tabular">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
439 <assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
440 <has_text text="class"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
441 <has_n_columns n="17"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
442 <has_n_lines n="1"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
443 </assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
444 </element>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
445 <element name="kingdom" ftype="tabular">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
446 <assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
447 <has_text text="kingdom_id"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
448 <has_n_columns n="3"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
449 <has_n_lines n="1"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
450 </assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
451 </element>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
452 <element name="phylum" ftype="tabular">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
453 <assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
454 <has_text text="phylum_id"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
455 <not_has_text text="kingdom_id"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
456 <has_n_columns n="3"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
457 <has_n_lines n="1"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
458 </assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
459 </element>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
460 <element name="class" ftype="tabular">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
461 <assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
462 <has_text text="class_id"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
463 <not_has_text text="phylum_id"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
464 <has_n_columns n="3"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
465 <has_n_lines n="1"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
466 </assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
467 </element>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
468 <element name="order" ftype="tabular">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
469 <assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
470 <has_text text="order_id"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
471 <not_has_text text="class_id"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
472 <has_n_columns n="3"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
473 <has_n_lines n="1"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
474 </assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
475 </element>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
476 <element name="family" ftype="tabular">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
477 <assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
478 <has_text text="family_id"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
479 <not_has_text text="order"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
480 <has_n_columns n="3"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
481 <has_n_lines n="1"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
482 </assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
483 </element>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
484 <element name="genus" ftype="tabular">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
485 <assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
486 <has_text text="genus_id"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
487 <not_has_text text="family"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
488 <has_n_columns n="3"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
489 <has_n_lines n="1"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
490 </assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
491 </element>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
492 <element name="species" ftype="tabular">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
493 <assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
494 <has_text text="species_id"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
495 <not_has_text text="genus"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
496 <has_n_columns n="3"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
497 <has_n_lines n="1"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
498 </assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
499 </element>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
500 <element name="strains" ftype="tabular">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
501 <assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
502 <has_text text="strains_id"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
503 <not_has_text text="species_id"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
504 <has_n_columns n="3"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
505 <has_n_lines n="1"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
506 </assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
507 </element>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
508 </output_collection>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
509 <output name="krona_output_file" ftype="tabular">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
510 <assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
511 <not_has_text text="k__Bacteria"/>
5
6dee4abadccb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6
iuc
parents: 3
diff changeset
512 <has_n_lines n="1" delta="1"/>
6dee4abadccb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6
iuc
parents: 3
diff changeset
513 <has_size value="1" delta="1"/>
2
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
514 </assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
515 </output>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
516 </test>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
517 <test expect_num_outputs="6">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
518 <section name="inputs">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
519 <conditional name="in">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
520 <param name="selector" value="raw"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
521 <conditional name="raw_in">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
522 <!-- Single GZ file -->
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
523 <param name="selector" value="single"/>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
524 <param name="in" value="SRS014464-Anterior_nares.fasta.gz"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
525 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
526 <param name="read_min_len" value="70"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
527 <section name="mapping">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
528 <param name="bt2_ps" value="sensitive"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
529 <param name="min_mapq_val" value="5"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
530 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
531 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
532 <conditional name="db">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
533 <!-- Cached db -->
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
534 <param name="db_selector" value="cached"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
535 <param name="cached_db" value="test-db-20210409"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
536 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
537 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
538 <section name="analysis">
1
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
539 <conditional name="analysis_type">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
540 <param name="t" value="rel_ab"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
541 <conditional name="tax_lev">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
542 <param name="tax_lev" value="a"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
543 <param name="split_levels" value="true"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
544 </conditional>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
545 </conditional>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
546 <param name="min_cu_len" value="2000"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
547 <param name="organism_profiling" value="add_viruses"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
548 <param name="stat" value="avg_g"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
549 <param name="stat_q" value="0.2"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
550 <param name="perc_nonzero" value="0.33"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
551 <param name="avoid_disqm" value="true"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
552 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
553 <section name="out">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
554 <param name="sample_id_key" value="SampleID"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
555 <param name="sample_id" value="Metaphlan_Analysis"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
556 <param name="use_group_representative" value="false"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
557 <param name="legacy_output" value="false"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
558 <param name="CAMI_format_output" value="false"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
559 <param name="unknown_estimation" value="false"/>
1
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
560 <param name="krona_output" value="true"/>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
561 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
562 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
563 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
564 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
565 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
566 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
567 <output name="bowtie2out" ftype="tabular" file="SRS014464-Anterior_nares-bowtie2out.tabular" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
568 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
569 <has_text text="HWI-EAS109_102883399:3:104:7342:14360/1"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
570 <has_text text="37637__U2I1U8__N579_01580"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
571 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
572 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
573 <output name="sam_output_file" ftype="sam" file="SRS014464-Anterior_nares.sam" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
574 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
575 <has_text text="SN:13076__A0A2I1PE66__CYJ72_10760"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
576 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
577 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
578 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
579 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
580 <has_text text="k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_lacunata"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
581 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
582 </output>
1
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
583 <output_collection name="levels" type="list" >
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
584 <element name="all" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
585 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
586 <has_text text="Gammaproteobacteria"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
587 <has_text text="Corynebacterium accolens"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
588 <has_n_columns n="17"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
589 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
590 </element>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
591 <element name="kingdom" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
592 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
593 <has_text text="kingdom_id"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
594 <has_text text="Bacteria"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
595 <has_n_columns n="3"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
596 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
597 </element>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
598 <element name="phylum" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
599 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
600 <has_text text="phylum_id"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
601 <not_has_text text="kingdom_id"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
602 <has_text text="Firmicutes"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
603 <has_n_columns n="3"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
604 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
605 </element>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
606 <element name="class" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
607 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
608 <has_text text="class_id"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
609 <not_has_text text="phylum_id"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
610 <has_text text="Actinobacteria"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
611 <has_n_columns n="3"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
612 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
613 </element>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
614 <element name="order" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
615 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
616 <has_text text="order_id"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
617 <not_has_text text="class_id"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
618 <has_text text="Propionibacteriales"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
619 <has_n_columns n="3"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
620 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
621 </element>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
622 <element name="family" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
623 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
624 <has_text text="family_id"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
625 <not_has_text text="order"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
626 <has_text text="Propionibacteriaceae"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
627 <has_n_columns n="3"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
628 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
629 </element>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
630 <element name="genus" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
631 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
632 <has_text text="genus_id"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
633 <not_has_text text="family"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
634 <has_text text="Cutibacterium"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
635 <has_n_columns n="3"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
636 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
637 </element>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
638 <element name="species" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
639 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
640 <has_text text="species_id"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
641 <not_has_text text="genus"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
642 <has_text text="Corynebacterium accolens"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
643 <has_n_columns n="3"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
644 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
645 </element>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
646 <element name="strains" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
647 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
648 <has_text text="strains_id"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
649 <not_has_text text="species_id"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
650 <has_n_columns n="3"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
651 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
652 </element>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
653 </output_collection>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
654 <output name="krona_output_file" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
655 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
656 <not_has_text text="k__Bacteria"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
657 <has_text text="Corynebacterium accolens"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
658 <has_n_columns n="9"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
659 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
660 </output>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
661 </test>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
662 <test expect_num_outputs="4">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
663 <section name="inputs">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
664 <conditional name="in">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
665 <param name="selector" value="raw"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
666 <conditional name="raw_in">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
667 <!-- Multiple GZ file -->
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
668 <param name="selector" value="multiple"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
669 <param name="in" value="SRS014464-Anterior_nares.fasta.gz,SRS014464-Anterior_nares.fasta.gz"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
670 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
671 <param name="read_min_len" value="70"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
672 <section name="mapping">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
673 <param name="bt2_ps" value="sensitive"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
674 <param name="min_mapq_val" value="5"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
675 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
676 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
677 <conditional name="db">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
678 <!-- Local db -->
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
679 <param name="db_selector" value="history"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
680 <param name="bowtie2db" value="test-db.fasta"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
681 <param name="mpa_pkl" value="test-db.json"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
682 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
683 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
684 <section name="analysis">
1
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
685 <conditional name="analysis_type">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
686 <param name="t" value="rel_ab"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
687 <conditional name="tax_lev">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
688 <param name="tax_lev" value="a"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
689 <param name="split_levels" value="false"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
690 </conditional>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
691 </conditional>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
692 <param name="min_cu_len" value="2000"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
693 <param name="organism_profiling" value="add_viruses"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
694 <param name="stat" value="avg_g"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
695 <param name="stat_q" value="0.2"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
696 <param name="perc_nonzero" value="0.33"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
697 <param name="avoid_disqm" value="true"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
698 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
699 <section name="out">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
700 <param name="sample_id_key" value="SampleID"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
701 <param name="sample_id" value="Metaphlan_Analysis"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
702 <param name="use_group_representative" value="false"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
703 <param name="legacy_output" value="false"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
704 <param name="CAMI_format_output" value="false"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
705 <param name="unknown_estimation" value="false"/>
1
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
706 <param name="krona_output" value="false"/>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
707 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
708 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
709 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
710 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
711 <has_text text="relative_abundance"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
712 <has_text text="NCBI_tax_id"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
713 <has_text text="clade_name"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
714 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
715 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
716 <output name="bowtie2out" ftype="tabular" file="SRS014464-Anterior_nares-two-inputs-bowtie2out.tabular" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
717 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
718 <has_text text="HWI-EAS109_102883399:3:104:7342:14360/1"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
719 <has_text text="37637__U2I1U8__N579_01580"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
720 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
721 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
722 <output name="sam_output_file" ftype="sam" file="SRS014464-Anterior_nares-two-inputs.sam" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
723 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
724 <has_text text="SN:13076__A0A2I1PE66__CYJ72_10760"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
725 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
726 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
727 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
728 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
729 <has_text text="k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_lacunata"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
730 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
731 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
732 </test>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
733 <test expect_num_outputs="4">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
734 <section name="inputs">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
735 <conditional name="in">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
736 <param name="selector" value="raw"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
737 <conditional name="raw_in">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
738 <!-- Paired GZ file -->
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
739 <param name="selector" value="paired"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
740 <param name="in_f" value="SRS014464-Anterior_nares.fasta.gz"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
741 <param name="in_r" value="SRS014464-Anterior_nares.fasta.gz"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
742 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
743 <param name="read_min_len" value="70"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
744 <section name="mapping">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
745 <param name="bt2_ps" value="sensitive"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
746 <param name="min_mapq_val" value="5"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
747 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
748 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
749 <conditional name="db">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
750 <!-- Cached db -->
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
751 <param name="db_selector" value="cached"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
752 <param name="cached_db" value="test-db-20210409"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
753 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
754 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
755 <section name="analysis">
1
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
756 <conditional name="analysis_type">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
757 <param name="t" value="rel_ab"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
758 <conditional name="tax_lev">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
759 <param name="tax_lev" value="a"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
760 <param name="split_levels" value="false"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
761 </conditional>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
762 </conditional>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
763 <param name="min_cu_len" value="2000"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
764 <param name="organism_profiling" value="add_viruses"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
765 <param name="stat" value="avg_g"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
766 <param name="stat_q" value="0.2"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
767 <param name="perc_nonzero" value="0.33"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
768 <param name="avoid_disqm" value="true"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
769 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
770 <section name="out">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
771 <param name="sample_id_key" value="SampleID"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
772 <param name="sample_id" value="Metaphlan_Analysis"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
773 <param name="use_group_representative" value="false"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
774 <param name="legacy_output" value="false"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
775 <param name="CAMI_format_output" value="false"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
776 <param name="unknown_estimation" value="false"/>
1
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
777 <param name="krona_output" value="false"/>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
778 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
779 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
780 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
781 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
782 <has_text text="relative_abundance"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
783 <has_text text="NCBI_tax_id"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
784 <has_text text="clade_name"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
785 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
786 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
787 <output name="bowtie2out" ftype="tabular" file="SRS014464-Anterior_nares-two-inputs-bowtie2out.tabular" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
788 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
789 <has_text text="HWI-EAS109_102883399:3:104:7342:14360/1"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
790 <has_text text="37637__U2I1U8__N579_01580"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
791 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
792 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
793 <output name="sam_output_file" ftype="sam" file="SRS014464-Anterior_nares-two-inputs.sam" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
794 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
795 <has_text text="SN:13076__A0A2I1PE66__CYJ72_10760"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
796 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
797 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
798 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
799 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
800 <has_text text="k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_lacunata"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
801 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
802 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
803 </test>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
804 <test expect_num_outputs="2">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
805 <section name="inputs">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
806 <conditional name="in">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
807 <!-- SAM -->
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
808 <param name="selector" value="sam"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
809 <param name="in" value="SRS014464-Anterior_nares.sam"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
810 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
811 <conditional name="db">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
812 <!-- Cached db -->
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
813 <param name="db_selector" value="cached"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
814 <param name="cached_db" value="test-db-20210409"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
815 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
816 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
817 <section name="analysis">
1
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
818 <conditional name="analysis_type">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
819 <param name="t" value="rel_ab"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
820 <conditional name="tax_lev">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
821 <param name="tax_lev" value="a"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
822 <param name="split_levels" value="false"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
823 </conditional>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
824 </conditional>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
825 <param name="min_cu_len" value="2000"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
826 <param name="organism_profiling" value="add_viruses"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
827 <param name="stat" value="avg_g"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
828 <param name="stat_q" value="0.2"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
829 <param name="perc_nonzero" value="0.33"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
830 <param name="avoid_disqm" value="true"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
831 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
832 <section name="out">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
833 <param name="sample_id_key" value="SampleID"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
834 <param name="sample_id" value="Metaphlan_Analysis"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
835 <param name="use_group_representative" value="false"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
836 <param name="legacy_output" value="false"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
837 <param name="CAMI_format_output" value="false"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
838 <param name="unknown_estimation" value="false"/>
1
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
839 <param name="krona_output" value="false"/>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
840 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
841 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
842 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
843 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
844 <has_text text="relative_abundance"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
845 <has_text text="NCBI_tax_id"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
846 <has_text text="clade_name"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
847 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
848 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
849 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
850 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
851 <has_text text="k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_lacunata"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
852 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
853 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
854 </test>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
855 <test expect_num_outputs="2">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
856 <section name="inputs">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
857 <conditional name="in">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
858 <!-- bowtie2out -->
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
859 <param name="selector" value="bowtie2out"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
860 <param name="in" value="SRS014464-Anterior_nares-bowtie2out.tabular"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
861 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
862 <conditional name="db">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
863 <!-- Cached db -->
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
864 <param name="db_selector" value="cached"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
865 <param name="cached_db" value="test-db-20210409"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
866 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
867 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
868 <conditional name="in">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
869 <param name="selector" value="bowtie2out"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
870 <param name="in" value="SRS014464-Anterior_nares-bowtie2out.tabular"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
871 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
872 <section name="mapping">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
873 <param name="bt2_ps" value="sensite"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
874 <param name="min_mapq_val" value="5"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
875 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
876 <section name="analysis">
1
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
877 <conditional name="analysis_type">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
878 <param name="t" value="rel_ab"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
879 <conditional name="tax_lev">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
880 <param name="tax_lev" value="a"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
881 <param name="split_levels" value="false"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
882 </conditional>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
883 </conditional>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
884 <param name="min_cu_len" value="2000"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
885 <param name="organism_profiling" value="add_viruses"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
886 <param name="stat" value="avg_g"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
887 <param name="stat_q" value="0.2"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
888 <param name="perc_nonzero" value="0.33"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
889 <param name="avoid_disqm" value="true"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
890 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
891 <section name="out">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
892 <param name="sample_id_key" value="SampleID"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
893 <param name="sample_id" value="Metaphlan_Analysis"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
894 <param name="use_group_representative" value="false"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
895 <param name="legacy_output" value="false"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
896 <param name="CAMI_format_output" value="false"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
897 <param name="unknown_estimation" value="false"/>
1
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
898 <param name="krona_output" value="false"/>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
899 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
900 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
901 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
902 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
903 <has_text text="relative_abundance"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
904 <has_text text="NCBI_tax_id"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
905 <has_text text="clade_name"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
906 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
907 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
908 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
909 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
910 <has_text text="k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_lacunata"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
911 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
912 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
913 </test>
1
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
914 <test expect_num_outputs="6">
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
915 <section name="inputs">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
916 <conditional name="in">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
917 <param name="selector" value="raw"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
918 <conditional name="raw_in">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
919 <!-- Single FASTA file -->
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
920 <param name="selector" value="single"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
921 <param name="in" value="SRS014464-Anterior_nares.fasta"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
922 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
923 <param name="read_min_len" value="70"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
924 <section name="mapping">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
925 <param name="bt2_ps" value="sensitive"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
926 <param name="min_mapq_val" value="5"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
927 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
928 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
929 <conditional name="db">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
930 <!-- Cached db -->
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
931 <param name="db_selector" value="cached"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
932 <param name="cached_db" value="test-db-20210409"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
933 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
934 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
935 <section name="analysis">
1
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
936 <conditional name="analysis_type">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
937 <param name="t" value="rel_ab"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
938 <conditional name="tax_lev">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
939 <param name="tax_lev" value="a"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
940 <param name="split_levels" value="true"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
941 </conditional>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
942 </conditional>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
943 <param name="min_cu_len" value="2000"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
944 <param name="organism_profiling" value="add_viruses"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
945 <param name="stat" value="avg_g"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
946 <param name="stat_q" value="0.2"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
947 <param name="perc_nonzero" value="0.33"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
948 <param name="ignore_markers" value="marker.txt"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
949 <param name="avoid_disqm" value="true"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
950 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
951 <section name="out">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
952 <param name="sample_id_key" value="SampleID"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
953 <param name="sample_id" value="Metaphlan_Analysis"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
954 <param name="use_group_representative" value="false"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
955 <param name="legacy_output" value="true"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
956 <param name="CAMI_format_output" value="false"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
957 <param name="unknown_estimation" value="false"/>
1
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
958 <param name="krona_output" value="true"/>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
959 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
960 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-legacy-abundances.tabular" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
961 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
962 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
963 <has_text text="SampleID"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
964 <has_text text="Metaphlan_Analysis"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
965 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
966 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
967 <output name="bowtie2out" ftype="tabular" file="SRS014464-Anterior_nares-bowtie2out.tabular" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
968 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
969 <has_text text="HWI-EAS109_102883399:3:104:7342:14360/1"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
970 <has_text text="37637__U2I1U8__N579_01580"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
971 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
972 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
973 <output name="sam_output_file" ftype="sam" file="SRS014464-Anterior_nares.sam" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
974 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
975 <has_text text="SN:13076__A0A2I1PE66__CYJ72_10760"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
976 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
977 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
978 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
979 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
980 <has_text text="k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_lacunata"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
981 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
982 </output>
1
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
983 <output_collection name="levels" type="list" >
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
984 <element name="all" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
985 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
986 <has_text text="Gammaproteobacteria"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
987 <has_text text="Corynebacterium accolens"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
988 <has_n_columns n="9"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
989 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
990 </element>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
991 <element name="kingdom" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
992 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
993 <has_text text="kingdom"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
994 <has_text text="Bacteria"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
995 <has_n_columns n="2"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
996 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
997 </element>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
998 <element name="phylum" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
999 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1000 <has_text text="phylum"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1001 <has_text text="Firmicutes"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1002 <has_n_columns n="2"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1003 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1004 </element>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1005 <element name="class" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1006 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1007 <has_text text="class"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1008 <has_text text="Actinobacteria"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1009 <has_n_columns n="2"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1010 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1011 </element>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1012 <element name="order" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1013 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1014 <has_text text="order"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1015 <has_text text="Propionibacteriales"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1016 <has_n_columns n="2"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1017 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1018 </element>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1019 <element name="family" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1020 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1021 <has_text text="family"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1022 <has_text text="Propionibacteriaceae"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1023 <has_n_columns n="2"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1024 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1025 </element>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1026 <element name="genus" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1027 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1028 <has_text text="genus"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1029 <has_text text="Cutibacterium"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1030 <has_n_columns n="2"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1031 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1032 </element>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1033 <element name="species" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1034 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1035 <has_text text="species"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1036 <has_text text="Corynebacterium accolens"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1037 <has_n_columns n="2"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1038 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1039 </element>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1040 <element name="strains" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1041 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1042 <has_text text="strains"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1043 <has_n_columns n="2"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1044 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1045 </element>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1046 </output_collection>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1047 <output name="krona_output_file" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1048 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1049 <not_has_text text="k__Bacteria"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1050 <has_text text="Corynebacterium accolens"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1051 <has_n_columns n="9"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1052 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
iuc
parents: 0
diff changeset
1053 </output>
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1054 </test>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1055 </tests>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1056 <help><![CDATA[
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1057 What it does
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1058 ============
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1059
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1060 MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria,
5
6dee4abadccb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6
iuc
parents: 3
diff changeset
1061 Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) at species-level.
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1062
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1063 MetaPhlAn relies on ~1.1M unique clade-specific marker genes identified from ~100,000 reference genomes
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1064 (~99,500 bacterial and archaeal and ~500 eukaryotic), allowing:
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1065
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1066 - unambiguous taxonomic assignments;
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1067 - accurate estimation of organismal relative abundance;
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1068 - species-level resolution for bacteria, archaea, eukaryotes and viruses;
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1069 - strain identification and tracking
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1070 - orders of magnitude speedups compared to existing methods.
2
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
1071 - microbiota strain-level population genomics
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1072
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1073 MetaPhlAn clade-abundance estimation
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1074 ------------------------------------
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1075
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1076 The basic usage of MetaPhlAn consists in the identification of the clades (from phyla to species and
2
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
iuc
parents: 1
diff changeset
1077 strains in particular cases) present in the microbiota obtained from a microbiome sample and their
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1078 relative abundance.
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1079
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1080 Marker level analysis
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1081 ---------------------
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1082
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1083 MetaPhlAn introduces the capability of characterizing organisms at the strain level using non
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1084 aggregated marker information. Such capability comes with several slightly different flavours and
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1085 are a way to perform strain tracking and comparison across multiple samples.
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1086
5
6dee4abadccb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6
iuc
parents: 3
diff changeset
1087 Usually, MetaPhlAn is first ran with default parameters for the type of analysis to profile the
6dee4abadccb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6
iuc
parents: 3
diff changeset
1088 species present in the community, and then a strain-level profiling can be performed to zoom-in on
0
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1089 specific species of interest. This operation can be performed quickly as it exploits the bowtie2out
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1090 intermediate file saved during the execution of the default analysis type.
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1091
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1092 Inputs
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1093 ======
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1094
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1095 Metaphlan takes as input either:
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff changeset
1096
5
6dee4abadccb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6
iuc
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1097 - one or several sequence files in Fasta, FastQ (whether compressed or not)
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f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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1098 - a BowTie2 produced SAM file
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a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
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1099 - an intermediary mapping file of the microbiota generated by a previous MetaPhlAn run
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f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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1100
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6dee4abadccb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6
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1101 It also needs the reference database, which can be locally installed or customized using the dedicated tools.
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f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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1102
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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1103 Outputs
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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1104 =======
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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1105
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6dee4abadccb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6
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1106 The main output is a tab-separated file with the predicted taxon relative abundances.
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f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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1107
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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1108 It also generates a BIOM file and some intermediate files (SAM and BowTie2out) if sequence files are given as inputs.
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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1109
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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1110
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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1111 More help and use cases
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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1112 =======================
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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1113
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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1114 To get more information about MetaPhlAn usage and use cases, please refer to the `Metaphlan documentation`_.
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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1115
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6dee4abadccb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6
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1116 .. _Metaphlan documentation: https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-4#Basic-Usage
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f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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1117
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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1118 ]]></help>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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1119 <expand macro="citations"/>
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ff8f55893e7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit edceb1050e9e312ef8b1201cee35992720667b6a"
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1120 </tool>