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comparison replicate_filter.xml @ 1:9fc2f24615a7 draft default tip

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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
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0:66453f08e258 1:9fc2f24615a7
2 <description> - Remove peaks that fail to appear in at least x-out-of-n (technical) replicates</description> 2 <description> - Remove peaks that fail to appear in at least x-out-of-n (technical) replicates</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="stdio" /> 7 <command detect_errors="exit_code">
8 <command><![CDATA[ 8 <![CDATA[
9 dimspy replicate-filter 9 dimspy replicate-filter
10 --input "$hdf5_file_in" 10 --input '$hdf5_file_in'
11 --output "$hdf5_file_out" 11 --output '$hdf5_file_out'
12 #if $filelist 12 #if $filelist
13 --filelist "$filelist" 13 --filelist '$filelist'
14 #end if 14 #end if
15 --ppm $ppm 15 --ppm $ppm
16 --replicates $replicates 16 --replicates $replicates
17 --min-peak-present $min_peaks 17 --min-peak-present $min_peaks
18 #if $rsd_threshold 18 #if $rsd_threshold
19 --rsd-threshold $rsd_threshold 19 --rsd-threshold $rsd_threshold
20 #end if 20 #end if
21 --report "$report" 21 --report '$report'
22 && 22 &&
23 dimspy create-sample-list 23 dimspy create-sample-list
24 --input "$hdf5_file_out" 24 --input '$hdf5_file_out'
25 --output "$samplelist" 25 --output '$samplelist'
26 --delimiter tab 26 --delimiter tab
27 && 27 &&
28 dimspy hdf5-pls-to-txt 28 dimspy hdf5-pls-to-txt
29 --input "$hdf5_file_out" 29 --input '$hdf5_file_out'
30 --output . 30 --output .
31 --delimiter $delimiter 31 --delimiter $delimiter
32 ]]></command> 32 ]]>
33 </command>
33 <inputs> 34 <inputs>
34 <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"/> 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"/>
35 <param name="filelist" type="data" optional="true" format="tsv,tabular" label="Filelist / Samplelist" argument="--filelist" /> 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" />
36 <param name="replicates" type="integer" value="3" label="Number of technical replicates" help="" argument="--replicates"/> 37 <param name="replicates" type="integer" value="3" label="Number of technical replicates for each sample" help="" argument="--replicates"/>
37 <param name="min_peaks" type="integer" value="2" label="Number of technical replicates a peak has to be present in" help="" argument="--min_peaks"/> 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"/>
38 <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"/> 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"/>
39 <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"/> 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"/>
40 <param name="delimiter" type="hidden" value="tab" argument="--delimiter"/> 41 <param name="delimiter" type="hidden" value="tab" argument="--delimiter"/>
41 </inputs> 42 </inputs>
42 <outputs> 43 <outputs>
106 **\2. Filelist / Samplelist** (OPTIONAL) 107 **\2. Filelist / Samplelist** (OPTIONAL)
107 108
108 | A tabular-formatted .txt file with columns: filename, replicate, batch, classLabel, injectionOrder. 109 | A tabular-formatted .txt file with columns: filename, replicate, batch, classLabel, injectionOrder.
109 | Additional collumns are allowed but are not used during processing. 110 | Additional collumns are allowed but are not used during processing.
110 | 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. 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.
111 | **NOTE:** Only provide a filelist if you like to exclude Peaklist or if you have not provided a filelist for 'process scans'. 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'.
112 | 113 |
113 114
114 @example_filelist@ 115 @example_filelist@
115 116
116 **\3. Number of technical replicates** (REQUIRED) 117 **\3. Number of technical replicates** (REQUIRED)
117 118
118 The total number of technical replicates acquired for each sample (all samples must have the same number of technical replicates) 119 The total number of technical replicates acquired for each sample (all samples must have the same number of technical replicates)
119 120
120 **\4. Number of technical replicates a peak has to be present in** (REQUIRED) 121 **\4. Minimum number of technical replicates a peak has to be present in** (REQUIRED)
121 122
122 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. 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.
123 124
124 **\5. ppm error tolerance** (REQUIRED) 125 **\5. ppm error tolerance** (REQUIRED)
125 126