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comparison align_samples.xml @ 2:7b6f148bd99f draft default tip

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"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 80069808371b58f45da0c8133c27d67ac1a5b448"
author computational-metabolomics
date Wed, 17 Feb 2021 10:57:52 +0000
parents c72868b80c29
children
comparison
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1:c72868b80c29 2:7b6f148bd99f
1 <tool id="dimspy_align_samples" name="Align Samples" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@"> 1 <tool id="dimspy_align_samples" name="Align Samples" version="@TOOL_VERSION@+galaxy1">
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" />
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 --ncpu \${GALAXY_SLOTS:-1}
17 --block-size $adv.block_size
16 #if $hdf5_to_txt.standard 18 #if $hdf5_to_txt.standard
17 && 19 &&
18 @HDF5_PM_TO_TXT@ 20 @HDF5_PM_TO_TXT@
19 #end if 21 #end if
20 #if $hdf5_to_txt.comprehensive 22 #if $hdf5_to_txt.comprehensive
27 <param name="hdf5_file_in" argument="--input" type="data" format="h5" label="Peaklists (HDF5 file)" help="" /> 29 <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." /> 30 <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)." /> 31 <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" /> 32 <param name="delimiter" argument="--delimiter" type="hidden" value="tab" />
31 <expand macro="hdf5_pm_to_txt" /> 33 <expand macro="hdf5_pm_to_txt" />
34 <section name="adv" title="Advanced options" expanded="False">
35 <param name="block_size" argument="--block-size" type="integer" value="5000" label="Block size" help="The size of each block of peaks to perform clustering on." />
36 </section>
32 </inputs> 37 </inputs>
33 <outputs> 38 <outputs>
34 <expand macro="outputs_peak_intensity_matrix" /> 39 <expand macro="outputs_peak_intensity_matrix" />
35 </outputs> 40 </outputs>
36 <tests> 41 <tests>
42 <param name="standard" value="True"/> 47 <param name="standard" value="True"/>
43 <param name="comprehensive" value="False"/> 48 <param name="comprehensive" value="False"/>
44 <param name="samples_representations" value="rows"/> 49 <param name="samples_representations" value="rows"/>
45 <param name="matrix_attr" value="intensity"/> 50 <param name="matrix_attr" value="intensity"/>
46 </conditional> 51 </conditional>
52 <output name="hdf5_file_out" file="pm_as.h5" ftype="h5" compare="sim_size"/>
53 <output name="matrix_file_out" file="peak_matrix_as.txt" ftype="tsv"/>
54 </test>
55 <test>
56 <param name="hdf5_file_in" value="pls_rf.h5" ftype="h5"/>
57 <param name="ppm" value="2.0"/>
58 <param name="delimiter" value="tab"/>
59 <conditional name="hdf5_to_txt" >
60 <param name="standard" value="True"/>
61 <param name="comprehensive" value="False"/>
62 <param name="samples_representations" value="rows"/>
63 <param name="matrix_attr" value="intensity"/>
64 </conditional>
65 <section name="adv">
66 <param name="block_size" value="10000"/>
67 </section>
47 <output name="hdf5_file_out" file="pm_as.h5" ftype="h5" compare="sim_size"/> 68 <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"/> 69 <output name="matrix_file_out" file="peak_matrix_as.txt" ftype="tsv"/>
49 </test> 70 </test>
50 <test> 71 <test>
51 <param name="hdf5_file_in" value="pls_rf.h5" ftype="h5"/> 72 <param name="hdf5_file_in" value="pls_rf.h5" ftype="h5"/>