Mercurial > repos > galaxyp > cardinal_filtering

comparison filtering.xml @ 9:e92efed83208 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 11:39:44 +0000
parents 1d4a6fe69a40
children a4475567dd22
comparison
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8:a8157342d9a3 9:e92efed83208
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 <requirement type="package" version="2.3">r-gridextra</requirement> 7 <requirement type="package" version="2.3">r-gridextra</requirement>
8 <requirement type="package" version="3.2.1">r-ggplot2</requirement> 8 <requirement type="package" version="3.3.2">r-ggplot2</requirement>
9 </expand> 9 </expand>
10 <expand macro="print_version"/> 10 <expand macro="print_version"/>
11 <command detect_errors="exit_code"> 11 <command detect_errors="exit_code">
12 <![CDATA[ 12 <![CDATA[
13 13
363 ggtitle("Spatial orientation of filtered pixels")+ 363 ggtitle("Spatial orientation of filtered pixels")+
364 theme_bw()+ 364 theme_bw()+
365 theme(plot.title = element_text(hjust = 0.5))+ 365 theme(plot.title = element_text(hjust = 0.5))+
366 theme(legend.position="bottom",legend.direction="vertical")+ 366 theme(legend.position="bottom",legend.direction="vertical")+
367 guides(fill=guide_legend(ncol=5,byrow=TRUE)) 367 guides(fill=guide_legend(ncol=5,byrow=TRUE))
368 print(pixel_image) 368 print(pixel_image + scale_fill_manual(values=c("#00BFC4", "#F8766D")))
369 369
370 370
371 ### visual mz feature control 371 ### visual mz feature control
372 372
373 kept_df = data.frame(mz(msidata), rep("remaining m/z", nrow(msidata))) 373 kept_df = data.frame(mz(msidata), rep("remaining m/z", nrow(msidata)))
382 geom_histogram()+ theme_bw()+ 382 geom_histogram()+ theme_bw()+
383 theme(plot.title = element_text(hjust = 0.5))+ 383 theme(plot.title = element_text(hjust = 0.5))+
384 theme(legend.position="bottom",legend.direction="vertical")+ 384 theme(legend.position="bottom",legend.direction="vertical")+
385 labs(title="Overview of filtered m/z", x="m/z", y = "count") + 385 labs(title="Overview of filtered m/z", x="m/z", y = "count") +
386 guides(fill=guide_legend(ncol=5,byrow=TRUE)) 386 guides(fill=guide_legend(ncol=5,byrow=TRUE))
387 print(histogram_mz) 387 print(histogram_mz + scale_fill_manual(values=c("#00BFC4", "#F8766D")))
388
388 389
389 390
390 dev.off() 391 dev.off()
391 392
392 ## save msidata as imzML file, will only work if there is at least 1 m/z left 393 ## save msidata as imzML file, will only work if there is at least 1 m/z left
523 </test> 524 </test>
524 <test> 525 <test>
525 <expand macro="processed_infile_imzml"/> 526 <expand macro="processed_infile_imzml"/>
526 <conditional name="processed_cond"> 527 <conditional name="processed_cond">
527 <param name="processed_file" value="processed"/> 528 <param name="processed_file" value="processed"/>
528 <param name="accuracy" value="100"/> 529 <param name="accuracy" value="200"/>
529 <param name="units" value="ppm"/> 530 <param name="units" value="ppm"/>
530 </conditional> 531 </conditional>
531 <param name="pixel_filtering" value="two_columns"/> 532 <param name="pixel_filtering" value="two_columns"/>
532 <param name="annotation_file" ftype="tabular" value="inputpixels_2column.tabular"/> 533 <param name="annotation_file" ftype="tabular" value="inputpixels_2column.tabular"/>
533 <param name="column_x" value="1"/> 534 <param name="column_x" value="1"/>