Mercurial > repos > galaxyp > cardinal_spectra_plots

comparison spectra_plots.xml @ 9:0b7e00e5b9d2 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
author galaxyp
date Thu, 24 Sep 2020 11:42:14 +0000
parents 64ea4507e0bd
children 10566783d718
comparison
equal deleted inserted replaced
8:ebb7de263d49 9:0b7e00e5b9d2
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 </macros> 7 </macros>
8 <expand macro="requirements"> 8 <expand macro="requirements">
9 <requirement type="package" version="3.2.1">r-ggplot2</requirement> 9 <requirement type="package" version="3.3.2">r-ggplot2</requirement>
10 <requirement type="package" version="2.3">r-gridextra</requirement> 10 <requirement type="package" version="2.3">r-gridextra</requirement>
11 <requirement type="package" version="1.0.0">r-scales</requirement> 11 <requirement type="package" version="1.1.1">r-scales</requirement>
12 </expand> 12 </expand>
13 <command detect_errors="exit_code"> 13 <command detect_errors="exit_code">
14 <![CDATA[ 14 <![CDATA[
15 @INPUT_LINKING@ 15 @INPUT_LINKING@
16 cat '${MSI_mzplots}' && 16 cat '${MSI_mzplots}' &&
454 </configfiles> 454 </configfiles>
455 <inputs> 455 <inputs>
456 <expand macro="reading_msidata"/> 456 <expand macro="reading_msidata"/>
457 <expand macro="pdf_filename"/> 457 <expand macro="pdf_filename"/>
458 <conditional name="pixel_conditional"> 458 <conditional name="pixel_conditional">
459 <param name="pixel_type" type="select" label="Choose spectra (pixel)"> 459 <param name="pixel_type" type="select" label="Choose spectra (pixel) and/or add spectra annotations">
460 <option value="all_pixel" selected="True" >All spectra</option> 460 <option value="all_pixel" selected="True" >All spectra</option>
461 <option value="tabular_pixel">Single spectra</option> 461 <option value="tabular_pixel">Single spectra</option>
462 </param> 462 </param>
463 <when value="tabular_pixel"> 463 <when value="tabular_pixel">
464 <param name="pixel_file" type="data" format="tabular" label="Load tabular file with pixel coordinates" 464 <param name="pixel_file" type="data" format="tabular" label="Load tabular file with pixel coordinates"
586 </test> 586 </test>
587 <test> 587 <test>
588 <expand macro="processed_infile_imzml"/> 588 <expand macro="processed_infile_imzml"/>
589 <conditional name="processed_cond"> 589 <conditional name="processed_cond">
590 <param name="processed_file" value="processed"/> 590 <param name="processed_file" value="processed"/>
591 <param name="accuracy" value="50"/> 591 <param name="accuracy" value="100"/>
592 <param name="units" value="ppm"/> 592 <param name="units" value="ppm"/>
593 </conditional> 593 </conditional>
594 <conditional name="pixel_conditional"> 594 <conditional name="pixel_conditional">
595 <param name="pixel_type" value="all_pixel"/> 595 <param name="pixel_type" value="all_pixel"/>
596 </conditional> 596 </conditional>