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comparison align_samples.xml @ 1:a941ec0fd2a4 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 09:16:29 -0400
parents 50a090761d51
children
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0:50a090761d51 1:a941ec0fd2a4
2 <description> - Align peaks across Peaklists</description> 2 <description> - Align peaks across Peaklists</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 align-samples 9 dimspy align-samples
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 #if $hdf5_to_txt.standard 16 #if $hdf5_to_txt.standard
17 && 17 &&
18 @HDF5_PM_TO_TXT@ 18 @HDF5_PM_TO_TXT@
19 #end if 19 #end if
20 #if $hdf5_to_txt.comprehensive 20 #if $hdf5_to_txt.comprehensive
21 && 21 &&
22 @HDF5_PM_TO_TXT_COMPREHENSIVE@ 22 @HDF5_PM_TO_TXT_COMPREHENSIVE@
23 #end if 23 #end if
24 ]]></command> 24 ]]>
25 </command>
25 <inputs> 26 <inputs>
26 <param name="hdf5_file_in" type="data" format="h5" label="Peaklists (HDF5 file)" help="" argument="--input"/> 27 <param name="hdf5_file_in" type="data" format="h5" label="Peaklists (HDF5 file)" help="" argument="--input"/>
27 <param name="filelist" type="data" optional="true" format="tsv,tabular" label="Filelist / Samplelist" argument="--filelist"/> 28 <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 or Replicate Filter." argument="--filelist"/>
28 <param name="ppm" type="float" value="2.0" label="ppm" help="Maximum tolerated m/z deviation across samples in parts per million (ppm)." argument="--ppm"/> 29 <param name="ppm" type="float" value="2.0" label="Ppm error tolerance" help="Maximum tolerated m/z deviation across samples in parts per million (ppm)." argument="--ppm"/>
29 <param name="delimiter" type="hidden" value="tab" argument="--delimiter"/> 30 <param name="delimiter" type="hidden" value="tab" argument="--delimiter"/>
30 <expand macro="hdf5_pm_to_txt" /> 31 <expand macro="hdf5_pm_to_txt" />
31 </inputs> 32 </inputs>
32 <outputs> 33 <outputs>
33 <expand macro="outputs_peak_intensity_matrix" /> 34 <expand macro="outputs_peak_intensity_matrix" />
91 **\2. Filelist / Samplelist** (OPTIONAL) 92 **\2. Filelist / Samplelist** (OPTIONAL)
92 93
93 | A tabular-formatted .txt file with columns: filename, batch, classLabel, injectionOrder. 94 | A tabular-formatted .txt file with columns: filename, batch, classLabel, injectionOrder.
94 | Additional collumns are allowed but are not used during processing. 95 | Additional collumns are allowed but are not used during processing.
95 | 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. 96 | 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.
96 | **NOTE:** Only provide a filelist if you like to exclude Peaklist or if you have not provided a filelist for 'Process Scans' or Replicate Filter'. 97 | **NOTE:** Only provide a filelist if you like to exclude Peaklist, update the metadata (e.g. classLabel), or if you have not provided a filelist for 'Process Scans' or Replicate Filter'.
97 | 98 |
98 99
99 <![CDATA[ 100 <![CDATA[
100 101
101 +-------------------------------+-------+------------+----------------+ 102 +-------------------------------+-------+------------+----------------+