Mercurial > repos > galaxyp > metaquantome

annotate metaquantome_expand.xml @ 1:47bfbd6597d0 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 636fd1c7e60779d1123056a2985d54881013d4cb
author galaxyp
date Wed, 05 Dec 2018 14:37:17 -0500
parents b17b03126d40
children 80ce9ca55697
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
1 <tool id="metaquantome_expand" name="MetaQuantome Expand" version="@VERSION@.0">
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
2 <description>annotated functional or taxonomy terms to include all terms</description>
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
3 <macros>
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
4 <import>macros.xml</import>
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
5 </macros>
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
6 <expand macro="requirements" />
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
8 mkdir -p data && #slurp
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
9 @MAKE_SAMPS_TSV@
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
10 metaquantome expand
1
47bfbd6597d0 planemo upload commit 636fd1c7e60779d1123056a2985d54881013d4cb
galaxyp
parents: 0
diff changeset
11 @EXPAND_PARAMS@
0
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
12 @DB_DIR@
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
13 #if $input.input_type == 'nopep':
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
14 --nopep --nopep_file='$input.nopep_file'
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
15 #else:
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
16 --int_file='$input.int_file'
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
17 --pep_colname_int='$input.pep_colname_int'
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
18 #end if
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
19 --outfile='$outfile'
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
20 ]]></command>
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
21 <inputs>
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
22 <expand macro="data_dir"/>
1
47bfbd6597d0 planemo upload commit 636fd1c7e60779d1123056a2985d54881013d4cb
galaxyp
parents: 0
diff changeset
23 <expand macro="expand_params"/>
0
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
24 <conditional name="input">
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
25 <param name="input_type" type="select" label="Select input data">
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
26 <option value="int">tabular intensity file with peptide column</option>
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
27 <option value="nopep">file without a peptide column</option>
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
28 </param>
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
29 <when value="int">
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
30 <param argument="--int_file" type="data" format="tabular" label="intensity data"
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
31 help=""/>
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
32 <param argument="--pep_colname_int" type="text" value="" label="Peptide column name"
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
33 help="The column name within the intensity file that corresponds to the peptide sequences">
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
34 <validator type="empty_field"/>
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
35 </param>
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
36 </when>
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
37 <when value="nopep">
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
38 <param argument="--nopep_file" type="data" format="tabular" label="intensity data"
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
39 help=""/>
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
40 </when>
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
41 </conditional>
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
42 <expand macro="output_samples_choice"/>
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
43 </inputs>
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
44 <outputs>
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
45 <data format="tabular" name="outfile" label="${tool.name} on ${on_string} expanded"/>
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
46 <expand macro="output_samples"/>
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
47 </outputs>
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
48 <tests>
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
49 <test>
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
50 <!-- expand('f', sinfo=TTEST_SINFO, int_file=int, pep_colname_int='peptide', pep_colname_func='peptide',
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
51 pep_colname_tax='peptide', data_dir=GO_TEST_DIR, outfile=expanded, func_file=func,
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
52 func_colname='go', ontology='go') -->
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
53 <param name="int_file" value="int_ttest.tab" ftype="tabular"/>
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
54 <param name="pep_colname_int" value="peptide" />
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
55 <param name="func_file" value="multiple_func.tab" />
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
56 <param name="pep_colname_func" value="peptide" />
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
57 <param name="func_colname" value="go"/>
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
58 <param name="mode" value="f" />
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
59 <param name="ontology" value="go" />
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
60 <param name="samps_src" value="build" />
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
61 <repeat name="samps">
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
62 <param name="group_name" value="s1"/>
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
63 <param name="col_names" value="int1,int2,int3"/>
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
64 </repeat>
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
65 <repeat name="samps">
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
66 <param name="group_name" value="s2"/>
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
67 <param name="col_names" value="int4,int5,int6"/>
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
68 </repeat>
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
69 <output name="outfile" file="go_expanded.tab" ftype="tabular"/>
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
70 </test>
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
71 </tests>
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
72 <help><![CDATA[
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
73 help
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
74 ]]></help>
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
75 <expand macro="citations" />
b17b03126d40 planemo upload commit c64c8aadb942f00c459963110d51558fad83d920-dirty
galaxyp
parents:
diff changeset
76 </tool>