Mercurial > repos > galaxyp > cardinal_preprocessing

comparison macros.xml @ 1:1b22c1e7bfe7 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
author galaxyp
date Thu, 25 Oct 2018 07:29:29 -0400
parents 8c05a34f160a
children 1b875f0b8024
comparison
equal deleted inserted replaced
0:8c05a34f160a 1:1b22c1e7bfe7
2 <token name="@VERSION@">1.12.1</token> 2 <token name="@VERSION@">1.12.1</token>
3 3
4 <xml name="requirements"> 4 <xml name="requirements">
5 <requirements> 5 <requirements>
6 <requirement type="package" version="@VERSION@">bioconductor-cardinal</requirement> 6 <requirement type="package" version="@VERSION@">bioconductor-cardinal</requirement>
7 <requirement type="package" version="3.5.1">r-base</requirement>
7 <yield/> 8 <yield/>
8 </requirements> 9 </requirements>
10 </xml>
11
12 <xml name="print_version">
13 <version_command><![CDATA[
14 echo $(R --version | grep version | grep -v GNU)", Cardinal version" $(R --vanilla --slave -e "library(Cardinal); cat(sessionInfo()\$otherPkgs\$Cardinal\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
15 ]]></version_command>
9 </xml> 16 </xml>
10 17
11 <token name="@INPUT_LINKING@"><![CDATA[ 18 <token name="@INPUT_LINKING@"><![CDATA[
12 #if $infile.ext == 'imzml' 19 #if $infile.ext == 'imzml'
13 ln -s '${infile.extra_files_path}/imzml' infile.imzML && 20 ln -s '${infile.extra_files_path}/imzml' infile.imzML &&
31 get(ls()[ls() != "fileName"]) 38 get(ls()[ls() != "fileName"])
32 } 39 }
33 40
34 #if $infile.ext == 'imzml' 41 #if $infile.ext == 'imzml'
35 #if str($processed_cond.processed_file) == "processed": 42 #if str($processed_cond.processed_file) == "processed":
36 msidata <- readImzML('infile', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units") 43 msidata <- readImzML('infile', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units", attach.only=TRUE)
37 centroided(msidata) = $centroids 44 centroided(msidata) = $centroids
38 #else 45 #else
39 msidata <- readImzML('infile') 46 msidata <- readImzML('infile', attach.only=TRUE)
40 centroided(msidata) = $centroids 47 centroided(msidata) = $centroids
41 #end if 48 #end if
42 #elif $infile.ext == 'analyze75' 49 #elif $infile.ext == 'analyze75'
43 msidata = readAnalyze('infile') 50 msidata = readAnalyze('infile', attach.only=TRUE)
44 centroided(msidata) = $centroids 51 centroided(msidata) = $centroids
45 #else 52 #else
46 msidata = loadRData('infile.RData') 53 msidata = loadRData('infile.RData')
47 #end if 54 #end if
48 55
175 182
176 <xml name="pdf_filename"> 183 <xml name="pdf_filename">
177 <param name="filename" type="text" value="" label="Title" help="Will appear in the pdf output, if nothing given it will take the dataset name"> 184 <param name="filename" type="text" value="" label="Title" help="Will appear in the pdf output, if nothing given it will take the dataset name">
178 <sanitizer invalid_char=""> 185 <sanitizer invalid_char="">
179 <valid initial="string.ascii_letters,string.digits"> 186 <valid initial="string.ascii_letters,string.digits">
180 <add value="_" /> 187 <add value="_"/>
188 <add value=" "/>
181 </valid> 189 </valid>
182 </sanitizer> 190 </sanitizer>
183 </param> 191 </param>
184 </xml> 192 </xml>
185 193
196 <param name="mz_tabular" type="data" format="tabular" label="@LABEL@" help="Only numeric m/z values are allowed"/> 204 <param name="mz_tabular" type="data" format="tabular" label="@LABEL@" help="Only numeric m/z values are allowed"/>
197 <param name="feature_column" data_ref="mz_tabular" label="Column with features" type="data_column"/> 205 <param name="feature_column" data_ref="mz_tabular" label="Column with features" type="data_column"/>
198 <param name="feature_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/> 206 <param name="feature_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
199 </xml> 207 </xml>
200 208
201 <xml name="reading_2_column_mz_tabular"> 209 <xml name="reading_2_column_mz_tabular" token_optional="false">
202 <param name="calibrant_file" type="data" optional="true" format="tabular" 210 <param name="calibrant_file" type="data" optional="@OPTIONAL@" format="tabular"
203 label="m/z of interest (e.g. internal Calibrants)" help="one column with m/z values, optional second column with names (m/z values can also be selected as name)"/> 211 label="m/z of interest (e.g. internal Calibrants)" help="one column with m/z values, optional second column with names (m/z values can also be selected as name)"/>
204 <param name="mz_column" data_ref="calibrant_file" label="Column with m/z values" type="data_column"/> 212 <param name="mz_column" data_ref="calibrant_file" optional="@OPTIONAL@" label="Column with m/z values" type="data_column"/>
205 <param name="name_column" data_ref="calibrant_file" label="Column with name of m/z values" type="data_column"/> 213 <param name="name_column" data_ref="calibrant_file" optional="@OPTIONAL@" label="Column with name of m/z values" type="data_column"/>
206 <param name="calibrant_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/> 214 <param name="calibrant_header" type="boolean" optional="@OPTIONAL@" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
207 </xml> 215 </xml>
208 216
209 <xml name="reading_pixel_annotations"> 217 <xml name="reading_pixel_annotations">
210 <param name="annotation_file" type="data" format="tabular" label="Tabular file with pixel coordinates and annotation" 218 <param name="annotation_file" type="data" format="tabular" label="Tabular file with pixel coordinates and annotation"
211 help="Tabular file with three columns: x values, y values and pixel annotations"/> 219 help="Tabular file with three columns: x values, y values and pixel annotations"/>