Galaxy | (sandbox for testing) |

Changeset 10:73656b244cfe (2018-01-15)

Previous changeset 9:de314813b7fe (2018-01-15) Next changeset 11:ba427b16556a (2018-01-15)

Commit message:
planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 87d951922e9b6ab518c55bf376d31fbb3ec2df8c

modified:
test-data/expected_dataMatrix.tsv
test-data/expected_variableMetadata.tsv
test-data/input_variableMetadata.tsv
w4mclassfilter.xml

diff -r de314813b7fe -r 73656b244cfe test-data/expected_dataMatrix.tsv
--- a/test-data/expected_dataMatrix.tsv Mon Jan 15 10:45:25 2018 -0500
+++ b/test-data/expected_dataMatrix.tsv Mon Jan 15 13:30:58 2018 -0500

@@ -1,16 +1,16 @@
HU_017 HU_034 HU_078 HU_091 HU_093 HU_099 HU_130 HU_134 HU_138
-HMDB03193 76043 44943 173175 242549 57066 559869 339188 471368 262271
-HMDB01101 30689 52217 229568 4763576 3878773 976436 608298 1605075 72021
-HMDB01101.1 6877586 3158 4763576 3878773 976436 831937 1605075 72021 442510
-HMDB10348 47259 60885 168264 176500 76457 610110 279156 524468 451573
-HMDB59717 357351 301983 1028110 1530493 270027 1378535 808334 1132813 871209
-HMDB13189 2644620 1661412 2755434 593863 837865 3526136 1608814 3446611 1941527
+HMDB00191 560002 575790 785428 645785 591569 960658 639437 1092885 1409045
+HMDB00208 747080 595872 3143654 4059767 1433702 5593888 2477288 3346077 4230072
+HMDB00251 368600 94936 293988 352855 767894 268331 310918 1248919 577184
HMDB00299 250551 456162 808657 614370 250403 768004 504108 1014041 1362408
-HMDB00191 560002 575790 785428 645785 591569 960658 639437 1092885 1409045
+HMDB00512 0 280560 556003 590779 209285 342532 569970 525240 246282
HMDB00518 0 85944 129886 175800 13154 230242 440223 315368 10657
HMDB00715 1252089 905408 5140022 2658555 814523 2558923 4184204 3865723 3236644
HMDB01032 2569205 1604999 26222916 257139 675754 59906109 31151730 18648127 14989438
-HMDB00208 747080 595872 3143654 4059767 1433702 5593888 2477288 3346077 4230072
+HMDB01101 30689 52217 229568 4763576 3878773 976436 608298 1605075 72021
+HMDB01101.1 6877586 3158 4763576 3878773 976436 831937 1605075 72021 442510
+HMDB03193 76043 44943 173175 242549 57066 559869 339188 471368 262271
HMDB04824 374028 539206 959381 605191 310260 1253319 477995 825691 1157093
-HMDB00512 0 280560 556003 590779 209285 342532 569970 525240 246282
-HMDB00251 368600 94936 293988 352855 767894 268331 310918 1248919 577184
+HMDB10348 47259 60885 168264 176500 76457 610110 279156 524468 451573
+HMDB13189 2644620 1661412 2755434 593863 837865 3526136 1608814 3446611 1941527
+HMDB59717 357351 301983 1028110 1530493 270027 1378535 808334 1132813 871209

diff -r de314813b7fe -r 73656b244cfe test-data/expected_variableMetadata.tsv
--- a/test-data/expected_variableMetadata.tsv Mon Jan 15 10:45:25 2018 -0500
+++ b/test-data/expected_variableMetadata.tsv Mon Jan 15 13:30:58 2018 -0500

@@ -1,16 +1,16 @@
-variableMetadata name
-HMDB03193 Testosterone_glucuronide
-HMDB01101 p-Anisic_acid
-HMDB01101.1 p-Anisic_acid_2
-HMDB10348 Dehydroepiandrosterone_3-glucuronide
-HMDB59717 Glu-Val
-HMDB13189 3-Indole_carboxylic_acid_glucuronide
-HMDB00299 Xanthosine
-HMDB00191 L-Aspartic_acid
-HMDB00518 Chenodeoxycholic_acid
-HMDB00715 Kynurenic_acid
-HMDB01032 Dehydroepiandrosterone_sulfate
-HMDB00208 Oxoglutaric_acid
-HMDB04824 N2,N2-Dimethylguanosine
-HMDB00512 N-Acetyl-L-phenylalanine
-HMDB00251 Taurine
+variableMetadata name mz rt
+HMDB00191 loquor 650 600
+HMDB00208 loquimini 873 476
+HMDB00251 pasamur 500 423
+HMDB00299 bantur 700 500
+HMDB00512 pantur 900 543
+HMDB00518 loquoris 870 250
+HMDB00715 loquitur 725 900
+HMDB01032 loquimur 550 425
+HMDB01101 bar 150 300
+HMDB01101.1 baz 200 225
+HMDB03193 foo 100 200
+HMDB04824 loquantur 950 522
+HMDB10348 batur 300 275
+HMDB13189 baris 800 325
+HMDB59717 bamur 125 400

diff -r de314813b7fe -r 73656b244cfe test-data/input_variableMetadata.tsv
--- a/test-data/input_variableMetadata.tsv Mon Jan 15 10:45:25 2018 -0500
+++ b/test-data/input_variableMetadata.tsv Mon Jan 15 13:30:58 2018 -0500

@@ -1,17 +1,17 @@
-variableMetadata name
-HMDB03193 Testosterone_glucuronide
-HMDB01101 p-Anisic_acid
-HMDB01101 p-Anisic_acid_2
-HMDB10348 Dehydroepiandrosterone_3-glucuronide
-HMDB59717 Glu-Val
-HMDB00822 p-Hydroxymandelic_acid
-HMDB13189 3-Indole_carboxylic_acid_glucuronide
-HMDB00299 Xanthosine
-HMDB00191 L-Aspartic_acid
-HMDB00518 Chenodeoxycholic_acid
-HMDB00715 Kynurenic_acid
-HMDB01032 Dehydroepiandrosterone_sulfate
-HMDB00208 Oxoglutaric_acid
-HMDB04824 N2,N2-Dimethylguanosine
-HMDB00512 N-Acetyl-L-phenylalanine
-HMDB00251 Taurine
+variable name mz rt
+HMDB03193 foo 100 200
+HMDB01101 bar 150 300
+HMDB01101 baz 200 225
+HMDB00208 loquimini 873 476
+HMDB10348 batur 300 275
+HMDB00299 bantur 700 500
+HMDB00191 loquor 650 600
+HMDB00518 loquoris 870 250
+HMDB59717 bamur 125 400
+HMDB00822 bamini 300 199
+HMDB13189 baris 800 325
+HMDB00715 loquitur 725 900
+HMDB01032 loquimur 550 425
+HMDB04824 loquantur 950 522
+HMDB00512 pantur 900 543
+HMDB00251 pasamur 500 423

diff -r de314813b7fe -r 73656b244cfe w4mclassfilter.xml
--- a/w4mclassfilter.xml Mon Jan 15 10:45:25 2018 -0500
+++ b/w4mclassfilter.xml Mon Jan 15 13:30:58 2018 -0500

b'@@ -23,7 +23,7 @@\n wildcards \'$wildcards\'\n classnameColumn \'$classnameColumn\'\n samplenameColumn \'$samplenameColumn\'\n- variable_range_filter \'$variable_range_filter\'\n+ variable_range_filter \'$variableRangeFilter\'\n dataMatrix_out \'$dataMatrix_out\'\n sampleMetadata_out \'$sampleMetadata_out\'\n variableMetadata_out \'$variableMetadata_out\'\n@@ -69,27 +69,13 @@\n <option value="FALSE" selected="true">filter-out</option>\n </param>\n \n- <param name="variable_range_filter" label="Variable range-filters" type="text" value = "" help="comma-separated filters specified as \'variableMetadataColumnName:min:max\'; default is no filters. (See help below.)">\n+ <param name="variableRangeFilter" label="Variable range-filters" type="text" value = "" help="comma-separated filters, each specified as \'variableMetadataColumnName:min:max\'; default is no filters. (See help below.)">\n <sanitizer>\n <valid initial="string.letters">\n <add preset="string.digits"/>\n- <add value="$" /> \n- <add value="(" /> \n- <add value=")" /> \n- <add value="*" /> \n- <add value="+" /> \n <add value="," /> \n- <add value="." /> \n <add value=":" /> \n- <add value=";" /> \n- <add value="?" /> \n- <add value="[" /> \n- <add value="\" /> \n- <add value="]" /> \n- <add value="^" /> \n- <add value="{" /> \n- <add value="|" /> \n- <add value="}" /> \n+ <add value="." /> \n </valid>\n </sanitizer>\n </param>\n@@ -106,6 +92,60 @@\n <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>\n <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>\n <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>\n+ <param name="classnameColumn" value="class"/>\n+ <param name="sampleclassNames" value=""/>\n+ <param name="wildcards" value="FALSE"/>\n+ <param name="samplenameColumn" value="sampleMetadata"/>\n+ <param name="inclusive" value="filter-out"/>\n+ <param name="variableRangeFilter" value="FEATMAX:2e6:,mz:200:,rt::800"/>\n+ <output name="sampleMetadata_out">\n+ <assert_contents>\n+ <has_text text="HU_028" />\n+ <has_text text="HU_051" />\n+ <has_text text="HU_060" />\n+ <has_text text="HU_110" />\n+ <has_text text="HU_149" />\n+ <has_text text="HU_152" />\n+ <has_text text="HU_175" />\n+ <has_text text="HU_178" />\n+ <has_text text="HU_185" />\n+ <not_has_text text="HU_204" />\n+ <has_text text="HU_208" />\n+ <has_text text="HU_017" />\n+ <has_text text="HU_034" />\n+ <has_text text="HU_078" />\n+ <has_text text="HU_091" />\n+ <has_text text="HU_093" />\n+ <has_text text="HU_099" />\n+ <has_text text="HU_130" />\n+ <has_text text="HU_134" />\n+ <has_text text="HU_138" />\n+ </assert_contents>\n+ </output>\n+ <output name="variableMetadata_out">\n+ <assert_contents>\n+ <has_text text="HMDB00191" />\n+ <has_text text="HMDB00208" />\n+ <not_has_text text="HMDB00251" />\n+ <not_has_text text="HMDB00299" />\n+ <not_has_text text="HMDB00512" />\n+ <not_has_text text="HMDB00518" />\n+ <not_has_text text="HMDB00715" />\n+ <not_has_text text="HMDB00822" />\n+ '..b"Matrix.tsv |\n++-------------------+---------------------------------------------------------------------------------------------------------------------------+\n+| Sample metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/expected_sampleMetadata.tsv |\n++-------------------+---------------------------------------------------------------------------------------------------------------------------+\n+| Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/expected_variableMetadata.tsv |\n++-------------------+---------------------------------------------------------------------------------------------------------------------------+\n \n .. class:: infomark\n \n@@ -627,7 +667,8 @@\n Running With Range-Filtering\n ----------------------------\n \n-This example retains only samples whose 'gender' attribute is 'M'.\n+This example retains only features whose mz is greater than 200, whose rt is less than 800, and whose maximum intensity across all samples is 2,000,000.\n+This example retains all samples (except those having zero variance for all feature), although it would be possible to filter on samples as well.\n \n **Input parameters**\n \n@@ -647,16 +688,15 @@\n \n **Expected outputs**\n \n-+-------------------+--------------------------------------------------------------------------------------------------------------------+\n-| Expected Output | Download from URL |\n-+===================+====================================================================================================================+\n-| Data matrix | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/rangefilter_dataMatrix.tsv |\n-+-------------------+--------------------------------------------------------------------------------------------------------------------+\n-| Sample metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/rangefilter_sampleMetadata.tsv |\n-+-------------------+--------------------------------------------------------------------------------------------------------------------+\n-| Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/rangefilter_variableMetadata.tsv |\n-+-------------------+--------------------------------------------------------------------------------------------------------------------+\n-\n++-------------------+------------------------------------------------------------------------------------------------------------------------------+\n+| Expected Output | Download from URL |\n++===================+==============================================================================================================================+\n+| Data matrix | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/rangefilter_dataMatrix.tsv |\n++-------------------+------------------------------------------------------------------------------------------------------------------------------+\n+| Sample metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/rangefilter_sampleMetadata.tsv |\n++-------------------+------------------------------------------------------------------------------------------------------------------------------+\n+| Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/rangefilter_variableMetadata.tsv |\n++-------------------+------------------------------------------------------------------------------------------------------------------------------+\n \n -----------------------------------------------------------------------------\n \n"