Mercurial > repos > galaxyp > cardinal_spectra_plots
diff test-data/preprocessing_results4.imzml @ 6:043f9c91f686 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
author | galaxyp |
---|---|
date | Wed, 25 Mar 2020 05:53:20 -0400 |
parents | 58c4aef16eb0 |
children | ebb7de263d49 |
line wrap: on
line diff
--- a/test-data/preprocessing_results4.imzml Fri Dec 13 13:52:57 2019 -0500 +++ b/test-data/preprocessing_results4.imzml Wed Mar 25 05:53:20 2020 -0400 @@ -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="{FE932E04-42E4-4D89-B721-2A6CE83250B6}" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="36C7C916C176DD85CBBF4B7FA969C92B9403768D" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="db79298c-8368-42d7-84fc-18cad6ef1924" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="18bae3cc87b4c9aab2577cffe2fbc7425a93270b" /> <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"> @@ -43,7 +42,7 @@ </sample> </sampleList> <softwareList count="1"> - <software id="Cardinal" version="1.12.1"> + <software id="Cardinal" version="2.4.0"> <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" /> </software> </softwareList> @@ -51,10 +50,16 @@ <scanSettings id="scansettings1"> <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="3" /> + <cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="3" /> + <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"> @@ -73,21 +78,23 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" /> + <userParam name="3DPositionX" value="1.000000" /> + <userParam name="3DPositionY" value="1.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> <binaryDataArray encodedLength="0"> <referenceableParamGroupRef ref="mzArray" /> <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" /> - <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="159" /> - <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="636" /> + <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1581" /> + <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="6324" /> <binary /> </binaryDataArray> <binaryDataArray encodedLength="0"> <referenceableParamGroupRef ref="intensityArray" /> - <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="652" /> - <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="159" /> - <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="636" /> + <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="6340" /> + <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1581" /> + <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="6324" /> <binary /> </binaryDataArray> </binaryDataArrayList> @@ -100,21 +107,23 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" /> + <userParam name="3DPositionX" value="2.000000" /> + <userParam name="3DPositionY" value="1.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> <binaryDataArray encodedLength="0"> <referenceableParamGroupRef ref="mzArray" /> <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" /> - <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="159" /> - <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="636" /> + <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1581" /> + <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="6324" /> <binary /> </binaryDataArray> <binaryDataArray encodedLength="0"> <referenceableParamGroupRef ref="intensityArray" /> - <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="1288" /> - <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="159" /> - <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="636" /> + <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="12664" /> + <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1581" /> + <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="6324" /> <binary /> </binaryDataArray> </binaryDataArrayList> @@ -127,21 +136,23 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" /> + <userParam name="3DPositionX" value="3.000000" /> + <userParam name="3DPositionY" value="1.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> <binaryDataArray encodedLength="0"> <referenceableParamGroupRef ref="mzArray" /> <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" /> - <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="159" /> - <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="636" /> + <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1581" /> + <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="6324" /> <binary /> </binaryDataArray> <binaryDataArray encodedLength="0"> <referenceableParamGroupRef ref="intensityArray" /> - <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="1924" /> - <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="159" /> - <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="636" /> + <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="18988" /> + <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1581" /> + <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="6324" /> <binary /> </binaryDataArray> </binaryDataArrayList> @@ -154,21 +165,23 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" /> + <userParam name="3DPositionX" value="1.000000" /> + <userParam name="3DPositionY" value="2.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> <binaryDataArray encodedLength="0"> <referenceableParamGroupRef ref="mzArray" /> <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" /> - <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="159" /> - <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="636" /> + <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1581" /> + <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="6324" /> <binary /> </binaryDataArray> <binaryDataArray encodedLength="0"> <referenceableParamGroupRef ref="intensityArray" /> - <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="2560" /> - <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="159" /> - <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="636" /> + <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="25312" /> + <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1581" /> + <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="6324" /> <binary /> </binaryDataArray> </binaryDataArrayList> @@ -181,21 +194,23 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" /> + <userParam name="3DPositionX" value="2.000000" /> + <userParam name="3DPositionY" value="2.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> <binaryDataArray encodedLength="0"> <referenceableParamGroupRef ref="mzArray" /> <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" /> - <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="159" /> - <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="636" /> + <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1581" /> + <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="6324" /> <binary /> </binaryDataArray> <binaryDataArray encodedLength="0"> <referenceableParamGroupRef ref="intensityArray" /> - <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="3196" /> - <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="159" /> - <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="636" /> + <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="31636" /> + <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1581" /> + <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="6324" /> <binary /> </binaryDataArray> </binaryDataArrayList> @@ -208,21 +223,23 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" /> + <userParam name="3DPositionX" value="3.000000" /> + <userParam name="3DPositionY" value="2.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> <binaryDataArray encodedLength="0"> <referenceableParamGroupRef ref="mzArray" /> <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" /> - <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="159" /> - <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="636" /> + <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1581" /> + <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="6324" /> <binary /> </binaryDataArray> <binaryDataArray encodedLength="0"> <referenceableParamGroupRef ref="intensityArray" /> - <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="3832" /> - <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="159" /> - <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="636" /> + <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="37960" /> + <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1581" /> + <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="6324" /> <binary /> </binaryDataArray> </binaryDataArrayList> @@ -235,21 +252,23 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" /> + <userParam name="3DPositionX" value="1.000000" /> + <userParam name="3DPositionY" value="3.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> <binaryDataArray encodedLength="0"> <referenceableParamGroupRef ref="mzArray" /> <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" /> - <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="159" /> - <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="636" /> + <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1581" /> + <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="6324" /> <binary /> </binaryDataArray> <binaryDataArray encodedLength="0"> <referenceableParamGroupRef ref="intensityArray" /> - <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="4468" /> - <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="159" /> - <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="636" /> + <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="44284" /> + <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1581" /> + <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="6324" /> <binary /> </binaryDataArray> </binaryDataArrayList> @@ -262,21 +281,23 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" /> + <userParam name="3DPositionX" value="2.000000" /> + <userParam name="3DPositionY" value="3.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> <binaryDataArray encodedLength="0"> <referenceableParamGroupRef ref="mzArray" /> <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" /> - <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="159" /> - <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="636" /> + <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1581" /> + <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="6324" /> <binary /> </binaryDataArray> <binaryDataArray encodedLength="0"> <referenceableParamGroupRef ref="intensityArray" /> - <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="5104" /> - <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="159" /> - <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="636" /> + <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="50608" /> + <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1581" /> + <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="6324" /> <binary /> </binaryDataArray> </binaryDataArrayList> @@ -289,21 +310,23 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" /> + <userParam name="3DPositionX" value="3.000000" /> + <userParam name="3DPositionY" value="3.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> <binaryDataArray encodedLength="0"> <referenceableParamGroupRef ref="mzArray" /> <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" /> - <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="159" /> - <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="636" /> + <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1581" /> + <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="6324" /> <binary /> </binaryDataArray> <binaryDataArray encodedLength="0"> <referenceableParamGroupRef ref="intensityArray" /> - <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="5740" /> - <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="159" /> - <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="636" /> + <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="56932" /> + <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1581" /> + <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="6324" /> <binary /> </binaryDataArray> </binaryDataArrayList>