Mercurial > repos > rjmw > dimspy_replicate_filter

annotate replicate_filter.xml @ 1:9fc2f24615a7 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 09:17:44 -0400
parents 66453f08e258
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
1 <tool id="dimspy_replicate_filter" name="Replicate Filter" version="1.0.0">
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
2 <description> - Remove peaks that fail to appear in at least x-out-of-n (technical) replicates</description>
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
3 <macros>
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
4 <import>macros.xml</import>
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
5 </macros>
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
6 <expand macro="requirements" />
1
9fc2f24615a7 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 42331bc61ea07d75f88007e5a2c65eaf9e811f06
rjmw
parents: 0
diff changeset
7 <command detect_errors="exit_code">
9fc2f24615a7 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 42331bc61ea07d75f88007e5a2c65eaf9e811f06
rjmw
parents: 0
diff changeset
8 <![CDATA[
0
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
9 dimspy replicate-filter
1
9fc2f24615a7 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 42331bc61ea07d75f88007e5a2c65eaf9e811f06
rjmw
parents: 0
diff changeset
10 --input '$hdf5_file_in'
9fc2f24615a7 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 42331bc61ea07d75f88007e5a2c65eaf9e811f06
rjmw
parents: 0
diff changeset
11 --output '$hdf5_file_out'
0
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
12 #if $filelist
1
9fc2f24615a7 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 42331bc61ea07d75f88007e5a2c65eaf9e811f06
rjmw
parents: 0
diff changeset
13 --filelist '$filelist'
0
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
14 #end if
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
15 --ppm $ppm
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
16 --replicates $replicates
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
17 --min-peak-present $min_peaks
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
18 #if $rsd_threshold
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
19 --rsd-threshold $rsd_threshold
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
20 #end if
1
9fc2f24615a7 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 42331bc61ea07d75f88007e5a2c65eaf9e811f06
rjmw
parents: 0
diff changeset
21 --report '$report'
0
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
22 &&
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
23 dimspy create-sample-list
1
9fc2f24615a7 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 42331bc61ea07d75f88007e5a2c65eaf9e811f06
rjmw
parents: 0
diff changeset
24 --input '$hdf5_file_out'
9fc2f24615a7 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 42331bc61ea07d75f88007e5a2c65eaf9e811f06
rjmw
parents: 0
diff changeset
25 --output '$samplelist'
0
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
26 --delimiter tab
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
27 &&
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
28 dimspy hdf5-pls-to-txt
1
9fc2f24615a7 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 42331bc61ea07d75f88007e5a2c65eaf9e811f06
rjmw
parents: 0
diff changeset
29 --input '$hdf5_file_out'
0
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
30 --output .
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
31 --delimiter $delimiter
1
9fc2f24615a7 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 42331bc61ea07d75f88007e5a2c65eaf9e811f06
rjmw
parents: 0
diff changeset
32 ]]>
9fc2f24615a7 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 42331bc61ea07d75f88007e5a2c65eaf9e811f06
rjmw
parents: 0
diff changeset
33 </command>
0
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
34 <inputs>
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
35 <param name="hdf5_file_in" type="data" format="h5" label="Peaklists (HDF5 file)" help="Peaklists generated by Process Scans (SIM-Stitch)." argument="--hdf5_file_in"/>
1
9fc2f24615a7 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 42331bc61ea07d75f88007e5a2c65eaf9e811f06
rjmw
parents: 0
diff changeset
36 <param name="filelist" type="data" optional="true" format="tsv,tabular" label="Filelist / Samplelist" help="Only provide a filelist if you like to exclude Peaklists, update the metadata (e.g. classLabel), or if you have not provided a filelist for Process Scans." argument="--filelist" />
9fc2f24615a7 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 42331bc61ea07d75f88007e5a2c65eaf9e811f06
rjmw
parents: 0
diff changeset
37 <param name="replicates" type="integer" value="3" label="Number of technical replicates for each sample" help="" argument="--replicates"/>
9fc2f24615a7 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 42331bc61ea07d75f88007e5a2c65eaf9e811f06
rjmw
parents: 0
diff changeset
38 <param name="min_peaks" type="integer" value="2" label="Minimum number of technical replicates a peak has to be present in" help="" argument="--min_peaks"/>
0
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
39 <param name="ppm" type="float" value="2.0" label="Ppm error tolerance" help="Maximum tolerated m/z deviation across technical replicates in parts per million (ppm)." argument="--ppm"/>
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
40 <param name="rsd_threshold" type="text" value="" label="Relative standard deviation threshold" help="Maximum tolerated relative standard deviation (RSD) of the peak intensities across technical replicates. Leave empty to skip this filter step." argument="--rsd-threshold"/>
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
41 <param name="delimiter" type="hidden" value="tab" argument="--delimiter"/>
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
42 </inputs>
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
43 <outputs>
66453f08e258 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 ${on_string}: Peaklists (HDF5 file)"/>
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
45 <data name="report" format="txt" label="${tool.name} on ${on_string}: Report"/>
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
46 <data name="samplelist" format="tsv" label="${tool.name} on ${on_string}: Sample Metadata (updated)" />
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
47 <collection name="peaklists_txt" type="list" label="${tool.name} on ${on_string}: Peaklists">
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
48 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tsv" directory="." visible="false" />
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
49 </collection>
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
50 </outputs>
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
51 <tests>
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
52 <test>
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
53 <param name="hdf5_file_in" value="pls.h5" ftype="h5"/>
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
54 <param name="replicates" value="3"/>
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
55 <param name="min_peaks" value="2"/>
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
56 <param name="ppm" value="2.0"/>
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
57 <param name="rsd_threshold" value=""/>
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
58 <output name="hdf5_file_out" value="pls_rf.h5" ftype="h5" compare="sim_size" />
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
59 <output name="report" value="report_pls_rf_01.txt" ftype="txt"/>
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
60 <output name="samplelist" value="samplelist_1.txt" ftype="tsv"/>
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
61 <output_collection name="peaklists_txt" type="list">
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
62 <element name="batch04_QC17_rep01_262_2_263_3_264" file="batch04_QC17_rep01_262_2_263_3_264.txt" ftype="tsv"/>
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
63 </output_collection>
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
64 </test>
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
65 <test>
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
66 <param name="hdf5_file_in" value="pls.h5" ftype="h5"/>
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
67 <param name="filelist" value="filelist_mzml_triplicates.txt" ftype="tsv"/>
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
68 <param name="replicates" value="3"/>
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
69 <param name="min_peaks" value="2"/>
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
70 <param name="ppm" value="2.0"/>
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
71 <param name="rsd_threshold" value=""/>
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
72 <output name="hdf5_file_out" value="pls_rf.h5" ftype="h5" compare="sim_size" />
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
73 <output name="report" value="report_pls_rf_02.txt" ftype="txt"/>
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
74 <output name="samplelist" value="samplelist_2.txt" ftype="tsv"/>
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
75 <output_collection name="peaklists_txt" type="list">
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
76 <element name="batch04_QC17_rep01_262_2_263_3_264" file="batch04_QC17_rep01_262_2_263_3_264.txt" ftype="tsv"/>
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
77 </output_collection>
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
78 </test>
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
79 </tests>
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
80 <help>
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
81 ----------------
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
82 Replicate filter
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
83 ----------------
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
84
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
85 |
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
86
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
87 Description
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
88 -----------
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
89
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
90 | This tools is typically applied following the 'process_scans' tool.
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
91 | Under the DIMS analysis workflow, biological samples are often analysed as a set of technical replicates. This tool is used to combine the Peaklists for each of these technical replicates, in to a single Peaklist.
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
92 |
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
93 | In combining technical replicate Peaklists, peaks are clustered together where the difference in their m/z values (measured in parts-per-million, 'ppm'), is less-than or equal to the user-defined threshold.
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
94 |
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
95 | Peaks are removed from final Peaklist if:
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
96
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
97 1) they occur in fewer than the user-defined 'Number of technical replicates a peak has to be present in' and/or
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
98 2) the relative standard deviation (measured in % and also termed the coefficient of variation) among intensity values for a peak is greater than the user-defined value.
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
99
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
100 Parameters
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
101 ----------
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
102
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
103 **\1. Set of Peaklists (HDF5 file)** (REQUIRED)
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
104
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
105 A set of Peaklists (HDF5 format). These files are automatically returned from the preceding 'process_scans' tool.
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
106
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
107 **\2. Filelist / Samplelist** (OPTIONAL)
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
108
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
109 | A tabular-formatted .txt file with columns: filename, replicate, batch, classLabel, injectionOrder.
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
110 | Additional collumns are allowed but are not used during processing.
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
111 | This file must be uploaded in to (or available from) the current history in order to allow for it to be selected from the drop-down menu.
1
9fc2f24615a7 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 42331bc61ea07d75f88007e5a2c65eaf9e811f06
rjmw
parents: 0
diff changeset
112 | **NOTE:** Only provide a filelist if you like to exclude Peaklists, update the metadata (e.g. classLabel), or if you have not provided a filelist for 'process scans'.
0
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
113 |
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
114
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
115 @example_filelist@
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
116
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
117 **\3. Number of technical replicates** (REQUIRED)
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
118
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
119 The total number of technical replicates acquired for each sample (all samples must have the same number of technical replicates)
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
120
1
9fc2f24615a7 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 42331bc61ea07d75f88007e5a2c65eaf9e811f06
rjmw
parents: 0
diff changeset
121 **\4. Minimum number of technical replicates a peak has to be present in** (REQUIRED)
0
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
122
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
123 A numerical value from 0 up to the numerical value entered in the 'Number of technical replicates' box. Peaks that occur in fewer than this number of technical replicates are removed from the output Peaklist.
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
124
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
125 **\5. ppm error tolerance** (REQUIRED)
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
126
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
127 A numerical value from 0 upwards. This values defines the tolerance applied when clustering peaks (based on their m/z value) across each of the technical replicates.
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
128
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
129 **\6. Relative standard deviation threshold** (OPTIONAL)
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
130
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
131 A numerical value from 0 upwards. Leave blank if you do not intend to apply a relative standard deviation threshold to your data.
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
132
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
133 Output file(s)
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
134 --------------
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
135
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
136 | A HDF5 file containing the replicate-filtered Peaklists
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
137 |
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
138 | A replicate-filtered Peaklist, in .tsv format, for each file specified in the filelist (Data Collection)
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
139
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
140 - Tab-delimited text file containing a numeric data matrix, with . as decimal, and NA for missing values.
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
141 - Includes additional information, such as the signal-to-noise ratio, relative-standard deviation (rsd) and 'purity' for each peak.
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
142
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
143 An **updated** filelist similar as described above
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
144
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
145 @github_developers_contributors@
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
146
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
147 </help>
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
148 <expand macro="citations" />
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
149 </tool>
66453f08e258 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
rjmw
parents:
diff changeset
150