Mercurial > repos > rjmw > dimspy_process_scans

annotate macros.xml @ 1:769165c75514 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 42331bc61ea07d75f88007e5a2c65eaf9e811f06
author rjmw
date Wed, 30 May 2018 09:20:20 -0400
parents d129e75a31d9
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
1 <macros>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
2 <xml name="requirements">
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
3 <requirements>
1
769165c75514 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 42331bc61ea07d75f88007e5a2c65eaf9e811f06
rjmw
parents: 0
diff changeset
4 <requirement type="package" version="1.2.0">dimspy</requirement>
0
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
5 </requirements>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
6 </xml>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
7
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
8 <token name="@HDF5_PM_TO_TXT@">
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
9 dimspy hdf5-pm-to-txt
1
769165c75514 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 42331bc61ea07d75f88007e5a2c65eaf9e811f06
rjmw
parents: 0
diff changeset
10 --input '$hdf5_file_out'
769165c75514 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 42331bc61ea07d75f88007e5a2c65eaf9e811f06
rjmw
parents: 0
diff changeset
11 --output '$matrix_file_out'
0
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
12 --delimiter $delimiter
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
13 --attribute_name $hdf5_to_txt.matrix_attr
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
14 --representation-samples $hdf5_to_txt.representation_samples
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
15 </token>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
16
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
17 <token name="@HDF5_PM_TO_TXT_COMPREHENSIVE@">
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
18 dimspy hdf5-pm-to-txt
1
769165c75514 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 42331bc61ea07d75f88007e5a2c65eaf9e811f06
rjmw
parents: 0
diff changeset
19 --input '$hdf5_file_out'
769165c75514 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 42331bc61ea07d75f88007e5a2c65eaf9e811f06
rjmw
parents: 0
diff changeset
20 --output '$matrix_comprehensive_file_out'
0
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
21 --delimiter $delimiter
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
22 --comprehensive
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
23 --attribute_name $hdf5_to_txt.matrix_attr
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
24 --representation-samples $hdf5_to_txt.representation_samples
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
25 </token>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
26
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
27 <xml name="hdf5_pm_to_txt">
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
28 <section name="hdf5_to_txt" title="Show options for addtional output (*.tsv files)" expanded="False">
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
29 <param name="standard" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Standard output?" help="Set to &quot;yes&quot; to produce a &quot;standard&quot; Peak Matrix (i.e. m/z and intensity)."/>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
30 <param name="comprehensive" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Comprehensive output?" help="Set to &quot;yes&quot; to produce a Peak Matrix with additional information (e.g. m/z and intensity, rsd, missing values)."/>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
31 <param name="representation_samples" type="select" label="Should the rows or columns represent the samples?">
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
32 <option value="rows" selected="true">Rows</option>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
33 <option value="columns">Columns</option>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
34 </param>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
35 <param name="matrix_attr" type="select" label="The Peak Matrix should contain ... values">
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
36 <option value="intensity" selected="true">Intensity</option>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
37 <option value="mz">m/z</option>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
38 <option value="snr">Signal-to-noise ratio (SNR)</option>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
39 </param>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
40 </section>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
41 </xml>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
42
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
43 <xml name="outputs_peak_intensity_matrix">
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
44 <data name="hdf5_file_out" format="h5" label="${tool.name} on ${on_string}: Peak Intensity Matrix (HDF5 file)"/>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
45 <data name="matrix_file_out" format="tsv" label="${tool.name} on ${on_string}: Peak Intensity Matrix">
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
46 <filter>hdf5_to_txt["standard"] is True</filter>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
47 </data>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
48 <data name="matrix_comprehensive_file_out" format="tsv" label="${tool.name} on ${on_string}: Peak Intensity Matrix (comprehensive)" >
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
49 <filter>hdf5_to_txt["comprehensive"] is True</filter>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
50 </data>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
51 </xml>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
52
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
53 <xml name="citations">
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
54 <citations>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
55 <citation type="doi">10.1038/nprot.2016.156</citation>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
56 <citation type="doi">10.1038/sdata.2014.12</citation>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
57 <citation type="doi">10.1021/ac062446p</citation>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
58 <citation type="doi">10.1021/ac2001803</citation>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
59 <yield />
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
60 </citations>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
61 </xml>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
62
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
63 <token name="@example_filelist@">
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
64 <![CDATA[
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
65
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
66 +-----------------+-----------+-------+------------+----------------+
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
67 | filename | replicate | batch | classLabel | injectionOrder |
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
68 +-----------------+-----------+-------+------------+----------------+
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
69 | sample_rep1.raw | 1 | 1 | sample | 1 |
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
70 +-----------------+-----------+-------+------------+----------------+
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
71 | sample_rep2.raw | 2 | 1 | sample | 2 |
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
72 +-----------------+-----------+-------+------------+----------------+
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
73 | sample_rep3.raw | 3 | 1 | sample | 3 |
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
74 +-----------------+-----------+-------+------------+----------------+
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
75 | sample_rep4.raw | 4 | 1 | sample | 4 |
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
76 +-----------------+-----------+-------+------------+----------------+
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
77 | blank_rep1.raw | 1 | 1 | blank | 5 |
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
78 +-----------------+-----------+-------+------------+----------------+
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
79 | blank_rep2.raw | 2 | 1 | blank | 6 |
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
80 +-----------------+-----------+-------+------------+----------------+
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
81 | blank_rep3.raw | 3 | 1 | blank | 7 |
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
82 +-----------------+-----------+-------+------------+----------------+
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
83 | blank_rep4.raw | 4 | 1 | blank | 8 |
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
84 +-----------------+-----------+-------+------------+----------------+
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
85 | ... | ... | ... | ... | ... |
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
86 +-----------------+-----------+-------+------------+----------------+
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
87
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
88 ]]>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
89 </token>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
90
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
91
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
92 <token name="@help_options_addtional_output@">
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
93 |
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
94 | **Show options for additonal output(s)** (OPTIONAL)
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
95 |
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
96
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
97 **\A. Standard output** (default = &quot;No&quot;)
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
98
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
99 Boolean toggle where selection of:
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
100
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
101 - &quot;Yes&quot; will generate a .txt formatted Peak Matrix (i.e. m/z and intensity).
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
102 - &quot;No&quot; will prevent the creation of a .txt formatted Peak Matrix.
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
103
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
104 **\B. Comprehensive output** (default = &quot;No&quot;)
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
105
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
106 Boolean toggle where selection of:
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
107
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
108 - &quot;Yes&quot; generates a Peak Matrix containing the m/z, intensity, missing values and other metrics associated with the aligned peaks.
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
109 - &quot;No&quot; will prevent the creation of a .txt formatted comprehensive Peak Matrix..
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
110
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
111 **\C. Should rows or columns represent the samples?** (default = &quot;rows&quot;)
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
112
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
113 Binary toggle (default = &quot;rows&quot;) where selection of:
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
114
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
115 - &quot;rows&quot; puts sample information in to the rows and m/z values (for aligned mass spectral peaks) in to columns of any output Peak Matrix.
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
116 - &quot;columns&quot; puts sample information in the columns and m/z values (for aligned mass spectral peaks) in to the rows of any output Peak Matrix.
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
117
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
118 **\D. The Peak Matrix should contain ... values**
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
119
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
120 Use this option to define which metric is inserted in to the cells of the output Peak Matrix.
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
121
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
122 - &quot;Intensity&quot; writes the absolute peak intensity to the Peak Matrix.
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
123 - &quot;m/z&quot; writes the m/z value to the Peak Matrix.
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
124 - &quot;Signal-to-noise ratio (SNR)&quot; writes the signal-to-noise ratio to the Peak Matrix.
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
125
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
126 Output file(s)
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
127 --------------
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
128
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
129 | A HDF5 file containing a Peak Matrix
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
130 |
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
131 | **OPTIONAL**
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
132 | A (standard and/or comprehenstive) Peak Matrix comprising samples on one axis and m/z values on the perpendicular axis
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
133 |
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
134
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
135 - Tab-delimited text file containing a numeric data matrix, with . as decimal, and NA for missing values.
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
136 - File only created if user toggles &quot;Standard output&quot; and/or &quot;Comprehensive output&quot; to &quot;Yes&quot;
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
137 - By default, samples are in rows and peaks are in columns. Altering the &quot;Should rows or columns represent samples&quot; toggle will transpose this matrix.
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
138
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
139 </token>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
140
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
141 <token name="@github_developers_contributors@">
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
142 Github respository (source code)
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
143 --------------------------------
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
144
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
145 https://github.com/computational-metabolomics/dimspy-galaxy/
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
146
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
147 Developers and contributors
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
148 ---------------------------
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
149
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
150 - **Ralf Weber (r.j.weber@bham.ac.uk) - University of Birmingham (UK)**
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
151 - **Martin R. Jones (m.r.jones.1@bham.ac.uk) - University of Birmingham (UK)**
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
152 - **Thomas Lawson (tnl495@bham.ac.uk) - University of Birmingham (UK)**
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
153
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
154 |
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
155 </token>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
156
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
157 </macros>