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comparison align_samples.xml @ 0:33b65dacd377 draft

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"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
author computational-metabolomics
date Sat, 11 Apr 2020 16:51:19 -0400
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children c72868b80c29
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-1:000000000000 0:33b65dacd377
1 <tool id="dimspy_align_samples" name="Align Samples" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
2 <description> - Align peaks across Peaklists</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code">
8 <![CDATA[
9 dimspy align-samples
10 --input '$hdf5_file_in'
11 --output '$hdf5_file_out'
12 #if $filelist
13 --filelist '$filelist'
14 #end if
15 --ppm $ppm
16 #if $hdf5_to_txt.standard
17 &&
18 @HDF5_PM_TO_TXT@
19 #end if
20 #if $hdf5_to_txt.comprehensive
21 &&
22 @HDF5_PM_TO_TXT_COMPREHENSIVE@
23 #end if
24 ]]>
25 </command>
26 <inputs>
27 <param name="hdf5_file_in" argument="--input" type="data" format="h5" label="Peaklists (HDF5 file)" help="" />
28 <param name="filelist" argument="--filelist" type="data" format="tsv,tabular" optional="true" 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 or Replicate Filter." />
29 <param name="ppm" argument="--ppm" type="float" value="2.0" label="Ppm error tolerance" help="Maximum tolerated m/z deviation across samples in parts per million (ppm)." />
30 <param name="delimiter" argument="--delimiter" type="hidden" value="tab" />
31 <expand macro="hdf5_pm_to_txt" />
32 </inputs>
33 <outputs>
34 <expand macro="outputs_peak_intensity_matrix" />
35 </outputs>
36 <tests>
37 <test>
38 <param name="hdf5_file_in" value="pls_rf.h5" ftype="h5"/>
39 <param name="ppm" value="2.0"/>
40 <param name="delimiter" value="tab"/>
41 <conditional name="hdf5_to_txt" >
42 <param name="standard" value="True"/>
43 <param name="comprehensive" value="False"/>
44 <param name="samples_representations" value="rows"/>
45 <param name="matrix_attr" value="intensity"/>
46 </conditional>
47 <output name="hdf5_file_out" file="pm_as.h5" ftype="h5" compare="sim_size"/>
48 <output name="matrix_file_out" file="peak_matrix_as.txt" ftype="tsv"/>
49 </test>
50 <test>
51 <param name="hdf5_file_in" value="pls_rf.h5" ftype="h5"/>
52 <param name="ppm" value="2.0"/>
53 <param name="delimiter" value="tab"/>
54 <conditional name="hdf5_to_txt">
55 <param name="standard" value="True"/>
56 <param name="comprehensive" value="False"/>
57 <param name="representation_samples" value="columns"/>
58 <param name="matrix_attr" value="intensity"/>
59 </conditional>
60 <output name="hdf5_file_out" file="pm_as.h5" ftype="h5" compare="sim_size"/>
61 <output name="matrix_file_out" file="peak_matrix_as_t.txt" ftype="tsv"/>
62 </test>
63 <test>
64 <param name="hdf5_file_in" value="pls_rf.h5" ftype="h5"/>
65 <param name="ppm" value="2.0"/>
66 <param name="delimiter" value="tab"/>
67 <conditional name="hdf5_to_txt">
68 <param name="standard" value="True"/>
69 <param name="comprehensive" value="True"/>
70 <param name="samples_representations" value="rows"/>
71 <param name="matrix_attr" value="mz"/>
72 </conditional>
73 <output name="hdf5_file_out" file="pm_as.h5" ftype="h5" compare="sim_size"/>
74 <output name="matrix_file_out" file="peak_matrix_as_mz.txt" ftype="tsv"/>
75 <output name="matrix_comprehensive_file_out" file="peak_matrix_as_mz_compr.txt" ftype="tsv"/>
76 </test>
77 </tests>
78 <help>
79 -------------
80 Align Samples
81 -------------
82
83 ..
84
85 -------------------------------
86
87 Description
88 -----------
89
90 Standard DIMS processing workflow: Process Scans -> Replicate Filter -> **Align Samples** -> [Missing values sample filter] -> Blank Filter -> Sample Filter -> Matrix processing -> Statistics
91
92 |
93
94 This tool takes the peaklists for all study samples and merges them in to single aligned peak matrix. The peak matrix comprises a table, with samples along one axis and the mass-to-charge ratios of detected mass spectral peaks along the opposite axis. At the intersection of sample and mass-to-charge ratio, the intensity is given for a specific peak in a specific sample (if no intensity recorded, then ‘0’ is inserted).
95
96 -------------------------------
97
98 Parameters
99 ----------
100
101 **Peaklists (HDF5 file)** (REQUIRED) - a HDF5 file containing all peaklists to undergo alignment.
102
103 |
104
105 **Filelist / Samplelist** (REQUIRED) - a file of type ‘tabular’ with the following required columns (additional metadata columns may also be included, e.g. “collectionTime”, etc.):
106
107 - **filename** - the name of the .raw or .mzML files from which peaklists were extracted using the “Process Scans” tool
108
109 - **batch** - a numeric value indicating the analysis batches samples were analysed in (if a single large analytica run then the default = 1)
110
111 - **classLabel** - a string indicating the experiment classes the samples belong to (e.g. control, QC, blank/placebo, exposed/treatment)
112
113 - **injectionOrder** - a numeric value indicating the order in which samples were analysed.
114
115 |
116
117 **ppm error tolerance** (REQUIRED; default = 2.0) - a numeric value equal-to or greater-than 0.
118
119 This parameter will influence the alignment of peaks from input peaklists. Peaks from distinct peaklists (corresponding to individual study samples) are aligned if the difference between their mass-to-charge ratios, when divided by the average of their mass-to-charge ratios and multiplied by 1 × 10\ :sup:`6` \, is equal-to or less-than than this parameter value (i.e. the difference between the mass-to-charge ratios, measured on the ppm scale, is less than the user-defined “ppm error tolerance”).
120
121 |
122
123 @help_options_addtional_output@
124
125 |
126
127 ------------------------------
128
129 Output file(s)
130 --------------
131
132 @help_outputs_matrix@
133
134 -------------------------------------------------------------
135
136 @github_developers_contributors@
137 @license@
138 </help>
139 <expand macro="citations" />
140 </tool>