Mercurial > repos > computational-metabolomics > dimspy_hdf5_to_txt

annotate hdf5_to_txt.xml @ 2:1b254abecb4a 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 80069808371b58f45da0c8133c27d67ac1a5b448"
author computational-metabolomics
date Wed, 17 Feb 2021 10:53:14 +0000
parents 5c545e1f0fa2
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
1 <tool id="dimspy_hdf5_to_txt" name="Convert DIMSpy-based HDF5 to tsv" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
2 <description></description>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
3 <macros>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
4 <import>macros.xml</import>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
5 </macros>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
6 <expand macro="requirements" />
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
7 <command detect_errors="exit_code">
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
8 <![CDATA[
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
9 #if $input.object_type == 'peak_lists'
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
10 dimspy hdf5-pls-to-txt
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
11 --input '$input.hdf5_file_in'
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
12 --output .
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
13 --delimiter $delimiter
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
14 #elif $input.object_type == 'peak_matrix'
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
15 #if $input.matrix_format == 'standard' or $input.matrix_format == 'standard_comprehensive'
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
16 dimspy hdf5-pm-to-txt
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
17 --input '$input.hdf5_file_in'
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
18 --output '$matrix_file_out'
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
19 --delimiter $delimiter
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
20 --attribute_name $input.matrix_attr
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
21 --representation-samples $input.representation_samples
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
22 #end if
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
23 #if $input.matrix_format == "standard_comprehensive"
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
24 &&
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
25 #end if
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
26 #if $input.matrix_format == 'comprehensive' or $input.matrix_format == 'standard_comprehensive'
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
27 dimspy hdf5-pm-to-txt
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
28 --input '$input.hdf5_file_in'
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
29 --output '$matrix_comprehensive_file_out'
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
30 --delimiter $delimiter
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
31 --comprehensive
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
32 --attribute_name '$input.matrix_attr'
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
33 --representation-samples $input.representation_samples
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
34 #end if
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
35 #end if
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
36 ]]>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
37 </command>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
38 <inputs>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
39 <param name="delimiter" argument="--delimiter" type="hidden" value="tab" />
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
40 <conditional name="input">
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
41 <param name="object_type" type="select" label="Content HDF5 file" help="">
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
42 <option value="peak_matrix" selected="true">Peak Intensity Matrix</option>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
43 <option value="peak_lists">Peak list(s)</option>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
44 </param>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
45 <when value="peak_lists">
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
46 <param name="hdf5_file_in" argument="--input" type="data" format="h5" label="Peaklist(s) (HDF5 file)" help="" />
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
47 </when>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
48 <when value="peak_matrix">
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
49 <param name="hdf5_file_in" argument="--input" type="data" format="h5" label="Peak intensity matrix (HDF5 file)" help="" />
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
50 <param name="matrix_format" type="select" label="Select format(s) tsv formatted peak instensity matrix" help="">
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
51 <option value="standard" selected="true">Standard Peak Matrix (i.e. m/z and intensity).</option>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
52 <option value="comprehensive">Comprehensive Peak Matrix (e.g. m/z and intensity, rsd, missing values).</option>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
53 <option value="standard_comprehensive">Standard and comprehensive</option>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
54 </param>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
55 <param name="representation_samples" type="select" label="Should the rows or columns represent the samples?" help="">
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
56 <option value="rows" selected="true">Rows</option>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
57 <option value="columns">Columns</option>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
58 </param>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
59 <param name="matrix_attr" type="select" label="The Peak Matrix should contain ... values" help="">
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
60 <option value="intensity" selected="true">Intensity</option>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
61 <option value="mz">m/z</option>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
62 <option value="snr">Signal-to-noise ratio (SNR)</option>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
63 </param>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
64 </when>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
65 </conditional>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
66 </inputs>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
67 <outputs>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
68 <collection name="peaklists_txt" type="list" label="${tool.name} on ${on_string}: Peaklists">
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
69 <filter>input["object_type"] == "peak_lists"</filter>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
70 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tsv" directory="." visible="false" />
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
71 </collection>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
72 <data name="matrix_file_out" format="tsv" label="${tool.name} on ${on_string}: Peak Matrix">
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
73 <filter>input["object_type"] == "peak_matrix" and (input["matrix_format"] == "standard" or input["matrix_format"] == "standard_comprehensive")</filter>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
74 </data>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
75 <data name="matrix_comprehensive_file_out" format="tsv" label="${tool.name} on ${on_string}: Peak Matrix (comprehensive)" >
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
76 <filter>input["object_type"] == "peak_matrix" and (input["matrix_format"] == "comprehensive" or input["matrix_format"] == "standard_comprehensive")</filter>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
77 </data>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
78 </outputs>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
79 <tests>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
80 <test>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
81 <conditional name="input">
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
82 <param name="object_type" value="peak_lists"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
83 <param name="hdf5_file_in" value="pls.h5" ftype="h5"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
84 </conditional>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
85 <output_collection name="peaklists_txt" type="list">
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
86 <element name="batch04_QC17_rep01_262" file="batch04_QC17_rep01_262.txt" ftype="tsv"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
87 <element name="batch04_QC17_rep02_263" file="batch04_QC17_rep02_263.txt" ftype="tsv"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
88 <element name="batch04_QC17_rep03_264" file="batch04_QC17_rep03_264.txt" ftype="tsv"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
89 </output_collection>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
90 </test>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
91 <test>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
92 <conditional name="input">
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
93 <param name="object_type" value="peak_matrix"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
94 <param name="hdf5_file_in" value="pm_as_bf_sf.h5" ftype="h5"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
95 <param name="matrix_format" value="comprehensive"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
96 <param name="representation_samples" value="columns"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
97 <param name="matrix_attr" value="intensity"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
98 </conditional>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
99 <output name="matrix_comprehensive_file_out" file="peak_matrix_hdf5_to_txt_intensity.txt" ftype="tsv"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
100 </test>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
101 <test>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
102 <conditional name="input">
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
103 <param name="object_type" value="peak_matrix"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
104 <param name="hdf5_file_in" value="pm_as_bf_sf.h5" ftype="h5"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
105 <param name="matrix_format" value="standard"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
106 <param name="representation_samples" value="rows"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
107 <param name="matrix_attr" value="mz"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
108 </conditional>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
109 <output name="matrix_file_out" file="peak_matrix_hdf5_to_txt_mz.txt" ftype="tsv"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
110 </test>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
111 <test>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
112 <conditional name="input">
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
113 <param name="object_type" value="peak_matrix"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
114 <param name="hdf5_file_in" value="pm_as_bf_sf.h5" ftype="h5"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
115 <param name="matrix_format" value="standard_comprehensive"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
116 <param name="representation_samples" value="rows"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
117 <param name="matrix_attr" value="snr"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
118 </conditional>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
119 <output name="matrix_file_out" file="peak_matrix_hdf5_to_txt_snr.txt" ftype="tsv"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
120 <output name="matrix_comprehensive_file_out" file="peak_matrix_hdf5_to_txt_comprehensive_snr.txt" ftype="tsv"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
121 </test>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
122 </tests>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
123 <help>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
124 --------------------------------
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
125 Convert DIMSpy-based HDF5 to tsv
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
126 --------------------------------
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
127
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
128 ..
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
129
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
130 ----------------------------------
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
131
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
132 Description
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
133 -----------
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
134
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
135 This tool converts a .hdf5 file, containing either peaklist(s) or a peak intensity matrix, to user-friendly .tsv file(s).
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
136
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
137 ----------------------------------
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
138
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
139 Parameters
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
140 ----------
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
141
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
142 **Contents of hdf5 file** (REQUIRED; default = **peak intensity matrix**) - selection menu in which the user defines whether the input .hdf5 file contains:
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
143
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
144 - **a peak intensity matrix**
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
145
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
146 - **peaklist(s)**
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
147
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
148 |
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
149
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
150 **Peak intensity matrix or peaklists (HDF5 file)** (REQUIRED) - selection menu in which the user chooses the .hdf5 file (from the active Galaxy history) to be converted to .tsv formatted output(s).
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
151
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
152 |
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
153
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
154 **Select format(s) tsv formatted peak intensity matrix** (REQUIRED; default = **Standard Peak Matrix**) - selection menu in which the user chooses from the following export options:
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
155
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
156 @help_options_addtional_output@
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
157
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
158 ----------------------------------
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
159
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
160 Output file(s)
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
161 --------------
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
162
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
163 **Important** - the metric recorded output peak matrix/matrices is adjusted using the "The peak matrix should contain intensity | m/z | SNR values" parameter. By default, samples are presented row-wise and peak mass-to-charge ratio values are presented column-wise in each peak matrix, though this may be adjusted using the "Should rows or columns represent samples" parameter toggle.
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
164
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
165 @help_outputs_matrix@
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
166
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
167 ----------------------------------------------
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
168
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
169 @github_developers_contributors@
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
170 @license@
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
171 </help>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
172 <expand macro="citations" />
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
173 </tool>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
174