Mercurial > repos > galaxyp > cardinal_preprocessing
changeset 5:ed9ed1e6cca2 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
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--- a/preprocessing.xml Fri Mar 22 08:12:42 2019 -0400 +++ b/preprocessing.xml Fri Dec 13 13:57:13 2019 -0500 @@ -494,7 +494,7 @@ <expand macro="reading_1_column_mz_tabular" label="Tabular file with m/z features to use for alignment. Only the m/z values from the tabular file will be kept."/> </when> <when value="align_msidata_ref"> - <param name="align_peaks_msidata" type="data" format="rdata," label="Picked and aligned Cardinal MSImageSet saved as RData"/> + <param name="align_peaks_msidata" type="data" format="rdata" label="Picked and aligned Cardinal MSImageSet saved as RData"/> </when> </conditional> </when> @@ -543,7 +543,7 @@ <expand macro="reading_1_column_mz_tabular" label="Tabular file with m/z features to extract from input file"/> </when> <when value="msidata_ref"> - <param name="peaks_msidata" type="data" format="rdata," label="Picked and aligned Cardinal MSImageSet saved as RData"/> + <param name="peaks_msidata" type="data" format="rdata" label="Picked and aligned Cardinal MSImageSet saved as RData"/> </when> </conditional> </when>
--- a/test-data/112_annotation_output.tabular Fri Mar 22 08:12:42 2019 -0400 +++ b/test-data/112_annotation_output.tabular Fri Dec 13 13:57:13 2019 -0500 @@ -1,16 +1,16 @@ -x y sample_name file_name column_name NA.x NA.y NA -1 1 msidata_1.RData file_one col1 NA NA NA -1 2 msidata_1.RData file_one col1 NA NA NA -1 3 msidata_1.RData file_one col1 NA NA NA -10 1 123_combined.RData file_two col3 NA NA NA -10 2 123_combined.RData file_two col3 NA NA NA -10 3 123_combined.RData file_two col3 NA NA NA -15 1 123_combined.RData file_three col3 NA NA NA -15 2 123_combined.RData file_three col3 NA NA NA -15 3 123_combined.RData file_three col3 NA NA NA -7 1 123_combined.RData file_one col1 NA NA NA -7 2 123_combined.RData file_one col1 NA NA NA -7 3 123_combined.RData file_one col1 NA NA NA -9 1 123_combined.RData file_two col2 NA NA NA -9 2 123_combined.RData file_two col2 NA NA NA -9 3 123_combined.RData file_two col2 NA NA NA +x y sample_name file_name column_name +1 1 msidata_1.RData file_one col1 +1 2 msidata_1.RData file_one col1 +1 3 msidata_1.RData file_one col1 +7 1 123_combined.RData file_one col1 +7 2 123_combined.RData file_one col1 +7 3 123_combined.RData file_one col1 +9 1 123_combined.RData file_two col2 +10 1 123_combined.RData file_two col3 +9 2 123_combined.RData file_two col2 +10 2 123_combined.RData file_two col3 +9 3 123_combined.RData file_two col2 +10 3 123_combined.RData file_two col3 +15 1 123_combined.RData file_three col3 +15 2 123_combined.RData file_three col3 +15 3 123_combined.RData file_three col3
--- a/test-data/112_auto_combined.imzml Fri Mar 22 08:12:42 2019 -0400 +++ b/test-data/112_auto_combined.imzml Fri Dec 13 13:57:13 2019 -0500 @@ -9,8 +9,8 @@ <fileContent> <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" /> <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" /> - <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{00A83E55-A8F8-41D4-BBAC-345FA77AAB7E}" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="9B17E43E3D3B35BE3CD0AE65F40E0C6B27C2752F" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="a0620366-fee2-4a2a-a643-0f0e0c9ae5a6" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="9bcd78ace1e6441dc527501b5eb3994fcf15b894" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> @@ -22,19 +22,18 @@ </referenceableParamGroup> <referenceableParamGroup id="scan1"> <cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" /> - <cvParam cvRef="MS" accession="MS:1000095" name="linear" value="" /> </referenceableParamGroup> <referenceableParamGroup id="mzArray"> <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" /> <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" /> <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" /> - <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" /> + <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" /> </referenceableParamGroup> <referenceableParamGroup id="intensityArray"> <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" /> <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" /> <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" /> - <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" /> + <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" /> </referenceableParamGroup> </referenceableParamGroupList> <sampleList count="1"> @@ -43,18 +42,24 @@ </sample> </sampleList> <softwareList count="1"> - <software id="Cardinal" version="1.12.1"> + <software id="Cardinal" version="2.2.6"> <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" /> </software> </softwareList> <scanSettingsList count="1"> <scanSettings id="scansettings1"> - <cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="15" /> + <cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="5" /> <cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3" /> + <cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="15" /> + <cvParam cvRef="IMS" accession="IMS:1000045" name="max dimension y" value="3" /> + <cvParam cvRef="IMS" accession="IMS:1000046" name="pixel size x" value="1.000000" /> + <cvParam cvRef="IMS" accession="IMS:1000047" name="pixel size y" value="1.000000" /> </scanSettings> </scanSettingsList> <instrumentConfigurationList count="1"> - <instrumentConfiguration id="IC1" /> + <instrumentConfiguration id="IC1"> + <cvParam cvRef="MS" accession="MS:1000031" name="instrument model" /> + </instrumentConfiguration> </instrumentConfigurationList> <dataProcessingList count="1"> <dataProcessing id="CardinalWriteImzML">
--- a/test-data/112_auto_combined.imzml.txt Fri Mar 22 08:12:42 2019 -0400 +++ b/test-data/112_auto_combined.imzml.txt Fri Dec 13 13:57:13 2019 -0500 @@ -1,4 +1,4 @@ imzML file: total 556 --rw-r--r-- 1 meli meli 537552 Feb 12 12:25 ibd --rw-r--r-- 1 meli meli 25466 Feb 12 12:25 imzml +-rw-r--r-- 1 meli meli 537552 Dez 11 00:10 ibd +-rw-r--r-- 1 meli meli 25811 Dez 11 00:10 imzml
--- a/test-data/123_annotation_output.tabular Fri Mar 22 08:12:42 2019 -0400 +++ b/test-data/123_annotation_output.tabular Fri Dec 13 13:57:13 2019 -0500 @@ -1,13 +1,13 @@ -x y sample_name file_name column_name NA.x NA.y NA -1 1 File1 file_one col1 NA NA NA -1 2 File1 file_one col1 NA NA NA -1 3 File1 file_one col1 NA NA NA -3 1 File2 file_two col2 NA NA NA -3 2 File2 file_two col2 NA NA NA -3 3 File2 file_two col2 NA NA NA -4 1 File2 file_two col3 NA NA NA -4 2 File2 file_two col3 NA NA NA -4 3 File2 file_two col3 NA NA NA -9 1 File3 file_three col3 NA NA NA -9 2 File3 file_three col3 NA NA NA -9 3 File3 file_three col3 NA NA NA +x y sample_name file_name column_name +1 1 File1 file_one col1 +1 2 File1 file_one col1 +1 3 File1 file_one col1 +3 1 File2 file_two col2 +4 1 File2 file_two col3 +3 2 File2 file_two col2 +4 2 File2 file_two col3 +3 3 File2 file_two col2 +4 3 File2 file_two col3 +9 1 File3 file_three col3 +9 2 File3 file_three col3 +9 3 File3 file_three col3
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--- a/test-data/123_combined_auto.imzml Fri Mar 22 08:12:42 2019 -0400 +++ b/test-data/123_combined_auto.imzml Fri Dec 13 13:57:13 2019 -0500 @@ -9,8 +9,8 @@ <fileContent> <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" /> <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" /> - <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{7DC9B0BB-277B-4A92-8780-2879E0E6A8F2}" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="6768CFB740661C3F0C560438B85A906EA05933D5" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="c12d4d26-5ff1-4c3c-99ea-95e0858faf36" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="147d6aa7f71a366246c93d750fcc9240b84c748f" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> @@ -22,19 +22,18 @@ </referenceableParamGroup> <referenceableParamGroup id="scan1"> <cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" /> - <cvParam cvRef="MS" accession="MS:1000095" name="linear" value="" /> </referenceableParamGroup> <referenceableParamGroup id="mzArray"> <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" /> <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" /> <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" /> - <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" /> + <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" /> </referenceableParamGroup> <referenceableParamGroup id="intensityArray"> <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" /> <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" /> <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" /> - <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" /> + <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" /> </referenceableParamGroup> </referenceableParamGroupList> <sampleList count="1"> @@ -43,18 +42,24 @@ </sample> </sampleList> <softwareList count="1"> - <software id="Cardinal" version="1.12.1"> + <software id="Cardinal" version="2.2.6"> <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" /> </software> </softwareList> <scanSettingsList count="1"> <scanSettings id="scansettings1"> - <cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="8" /> - <cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="11" /> + <cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="3" /> + <cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="6" /> + <cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="8" /> + <cvParam cvRef="IMS" accession="IMS:1000045" name="max dimension y" value="11" /> + <cvParam cvRef="IMS" accession="IMS:1000046" name="pixel size x" value="1.000000" /> + <cvParam cvRef="IMS" accession="IMS:1000047" name="pixel size y" value="1.000000" /> </scanSettings> </scanSettingsList> <instrumentConfigurationList count="1"> - <instrumentConfiguration id="IC1" /> + <instrumentConfiguration id="IC1"> + <cvParam cvRef="MS" accession="MS:1000031" name="instrument model" /> + </instrumentConfiguration> </instrumentConfigurationList> <dataProcessingList count="1"> <dataProcessing id="CardinalWriteImzML">
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picked.imzml.txt Fri Dec 13 13:57:13 2019 -0500 @@ -0,0 +1,4 @@ +imzML file: +total 192 +-rw-r--r-- 1 meli meli 157984 Dez 11 00:03 ibd +-rw-r--r-- 1 meli meli 35012 Dez 11 00:03 imzml
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