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Changeset 1:65ef413a35f3 (2018-10-25)

Previous changeset 0:28ba52c9548c (2018-10-01) Next changeset 2:e30d8b72415f (2019-02-15)

Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c

modified:
macros.xml
test-data/Heatmaps_LM8_file16.pdf
test-data/Heatmaps_analyze75.pdf
test-data/Heatmaps_imzml.pdf
test-data/Heatmaps_rdata.pdf
test-data/Plot_analyze75.pdf
test-data/Plot_analyze75_allpixels.pdf
test-data/Plot_empty_spectra.pdf
test-data/Plot_imzml.pdf
test-data/Plot_rdata.pdf
test-data/QC_analyze75.pdf
test-data/QC_empty_spectra.pdf
test-data/QC_imzml.pdf
test-data/QC_rdata.pdf
test-data/analyze75.svg
test-data/analyze75_filtered2.pdf
test-data/analyze_filteredoutside.RData
test-data/centroids_rdata.pdf
test-data/cluster_skm.RData
test-data/imzml_filtered3.RData
test-data/imzml_filtered3.pdf
test-data/imzml_filtered4.RData
test-data/imzml_filtered4.pdf
test-data/imzml_filtered5.RData
test-data/imzml_filtered5.pdf
test-data/kmeans_analyze.pdf
test-data/pca_imzml.pdf
test-data/rdata_notfiltered.RData
test-data/rdata_notfiltered.pdf
test-data/test1.pdf
test-data/test2.pdf
test-data/test2.rdata
test-data/test3.pdf
test-data/test4.pdf
test-data/test4.rdata
test-data/test5.pdf
test-data/test6.pdf
test-data/test6.rdata
test-data/test7.pdf
test-data/test7.rdata

removed:
test-data/imzml_filtered2.RData
test-data/imzml_filtered2.pdf

diff -r 28ba52c9548c -r 65ef413a35f3 macros.xml
--- a/macros.xml Mon Oct 01 01:05:33 2018 -0400
+++ b/macros.xml Thu Oct 25 07:26:29 2018 -0400

[

@@ -4,10 +4,17 @@
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@VERSION@">bioconductor-cardinal</requirement>
+            <requirement type="package" version="3.5.1">r-base</requirement>
             <yield/>
         </requirements>
     </xml>

+    <xml name="print_version">
+        <version_command><![CDATA[
+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: ")
+        ]]></version_command>
+    </xml>
+
     <token name="@INPUT_LINKING@"><![CDATA[
         #if $infile.ext == 'imzml'
             ln -s '${infile.extra_files_path}/imzml' infile.imzML &&
@@ -33,14 +40,14 @@

         #if $infile.ext == 'imzml'
             #if str($processed_cond.processed_file) == "processed":
-                msidata <- readImzML('infile', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units")
+                msidata <- readImzML('infile', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units", attach.only=TRUE)
                 centroided(msidata) = $centroids
             #else
-                msidata <- readImzML('infile')
+                msidata <- readImzML('infile', attach.only=TRUE)
                 centroided(msidata) = $centroids
             #end if
         #elif $infile.ext == 'analyze75'
-            msidata = readAnalyze('infile')
+            msidata = readAnalyze('infile', attach.only=TRUE)
             centroided(msidata) = $centroids
         #else
             msidata = loadRData('infile.RData')
@@ -177,7 +184,8 @@
         <param name="filename" type="text" value="" label="Title" help="Will appear in the pdf output, if nothing given it will take the dataset name">
             <sanitizer invalid_char="">
                 <valid initial="string.ascii_letters,string.digits">
-                    <add value="_" />
+                    <add value="_"/>
+                    <add value=" "/>
                 </valid>
             </sanitizer>
         </param>
@@ -198,12 +206,12 @@
         <param name="feature_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
     </xml>

-    <xml name="reading_2_column_mz_tabular">
-        <param name="calibrant_file" type="data" optional="true" format="tabular"
+    <xml name="reading_2_column_mz_tabular" token_optional="false">
+        <param name="calibrant_file" type="data" optional="@OPTIONAL@" format="tabular"
             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)"/>
-        <param name="mz_column" data_ref="calibrant_file" label="Column with m/z values" type="data_column"/>
-        <param name="name_column" data_ref="calibrant_file" label="Column with name of m/z values" type="data_column"/>
-        <param name="calibrant_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
+        <param name="mz_column" data_ref="calibrant_file" optional="@OPTIONAL@" label="Column with m/z values" type="data_column"/>
+        <param name="name_column" data_ref="calibrant_file" optional="@OPTIONAL@" label="Column with name of m/z values" type="data_column"/>
+        <param name="calibrant_header" type="boolean" optional="@OPTIONAL@" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
     </xml>

     <xml name="reading_pixel_annotations">

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diff -r 28ba52c9548c -r 65ef413a35f3 test-data/analyze75.svg
--- a/test-data/analyze75.svg Mon Oct 01 01:05:33 2018 -0400
+++ b/test-data/analyze75.svg Thu Oct 25 07:26:29 2018 -0400

@@ -1,15 +1,15 @@
<?xml version="1.0" encoding="UTF-8"?>
-<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="216pt" height="216pt" viewBox="0 0 216 216" version="1.1">
+<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="504pt" height="504pt" viewBox="0 0 504 504" version="1.1">
<g id="surface1">
-<rect x="0" y="0" width="216" height="216" style="fill:rgb(100%,100%,100%);fill-opacity:1;stroke:none;"/>
-<path style=" stroke:none;fill-rule:nonzero;fill:rgb(0%,100%,80%);fill-opacity:1;" d="M 0 0 L 72 0 L 72 72 L 0 72 Z M 0 0 "/>
-<path style=" stroke:none;fill-rule:nonzero;fill:rgb(0%,100%,32.156863%);fill-opacity:1;" d="M 0 72 L 72 72 L 72 144 L 0 144 Z M 0 72 "/>
-<path style=" stroke:none;fill-rule:nonzero;fill:rgb(100%,3.921569%,0%);fill-opacity:1;" d="M 0 144 L 72 144 L 72 216 L 0 216 Z M 0 144 "/>
-<path style=" stroke:none;fill-rule:nonzero;fill:rgb(0%,0%,0%);fill-opacity:1;" d="M 72 0 L 144 0 L 144 72 L 72 72 Z M 72 0 "/>
-<path style=" stroke:none;fill-rule:nonzero;fill:rgb(0%,0.392157%,33.333333%);fill-opacity:1;" d="M 72 72 L 144 72 L 144 144 L 72 144 Z M 72 72 "/>
-<path style=" stroke:none;fill-rule:nonzero;fill:rgb(0%,1.568627%,93.72549%);fill-opacity:1;" d="M 72 144 L 144 144 L 144 216 L 72 216 Z M 72 144 "/>
-<path style=" stroke:none;fill-rule:nonzero;fill:rgb(0%,0.784314%,54.509804%);fill-opacity:1;" d="M 144 0 L 216 0 L 216 72 L 144 72 Z M 144 0 "/>
-<path style=" stroke:none;fill-rule:nonzero;fill:rgb(0%,1.568627%,81.568627%);fill-opacity:1;" d="M 144 72 L 216 72 L 216 144 L 144 144 Z M 144 72 "/>
-<path style=" stroke:none;fill-rule:nonzero;fill:rgb(0%,1.960784%,100%);fill-opacity:1;" d="M 144 144 L 216 144 L 216 216 L 144 216 Z M 144 144 "/>
+<rect x="0" y="0" width="504" height="504" style="fill:rgb(100%,100%,100%);fill-opacity:1;stroke:none;"/>
+<path style=" stroke:none;fill-rule:nonzero;fill:rgb(0%,100%,80%);fill-opacity:1;" d="M 0 504 L 168 504 L 168 336 L 0 336 Z M 0 504 "/>
+<path style=" stroke:none;fill-rule:nonzero;fill:rgb(0%,100%,32.156863%);fill-opacity:1;" d="M 0 336 L 168 336 L 168 168 L 0 168 Z M 0 336 "/>
+<path style=" stroke:none;fill-rule:nonzero;fill:rgb(100%,3.921569%,0%);fill-opacity:1;" d="M 0 168 L 168 168 L 168 0 L 0 0 Z M 0 168 "/>
+<path style=" stroke:none;fill-rule:nonzero;fill:rgb(0%,0%,0%);fill-opacity:1;" d="M 168 504 L 336 504 L 336 336 L 168 336 Z M 168 504 "/>
+<path style=" stroke:none;fill-rule:nonzero;fill:rgb(0%,0.392157%,33.333333%);fill-opacity:1;" d="M 168 336 L 336 336 L 336 168 L 168 168 Z M 168 336 "/>
+<path style=" stroke:none;fill-rule:nonzero;fill:rgb(0%,1.568627%,93.72549%);fill-opacity:1;" d="M 168 168 L 336 168 L 336 0 L 168 0 Z M 168 168 "/>
+<path style=" stroke:none;fill-rule:nonzero;fill:rgb(0%,0.784314%,54.509804%);fill-opacity:1;" d="M 336 504 L 504 504 L 504 336 L 336 336 Z M 336 504 "/>
+<path style=" stroke:none;fill-rule:nonzero;fill:rgb(0%,1.568627%,81.568627%);fill-opacity:1;" d="M 336 336 L 504 336 L 504 168 L 336 168 Z M 336 336 "/>
+<path style=" stroke:none;fill-rule:nonzero;fill:rgb(0%,1.960784%,100%);fill-opacity:1;" d="M 336 168 L 504 168 L 504 0 L 336 0 Z M 336 168 "/>
</g>
</svg>

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