Merge pull request #6 from workflow4metabolomics/fix_combine_intval

Fix combine intval

galaxy/camera_annotate/planemo_test.sh

@@ -1,3 +1,10 @@
+# Example of planemo command to launch test
+
+# Note: --galaxy_branch "dev" is set to deal with zip file
+
+
+# -- Use of installed package environments
+# after having installing package on a local galaxy instance
 source /w/galaxy/dev/shed_tools_tool_dependency_dir/R/3.1.2/iuc/package_r_3_1_2/1ca39eb16186/env.sh
 source /w/galaxy/dev/shed_tools_tool_dependency_dir/bioconductor-camera/1.22.0/lecorguille/package_bioconductor_camera_1_22_0/22cec61d66c2/env.sh
 planemo test --install_galaxy --galaxy_branch "dev"
@@ -6,6 +13,16 @@ planemo test --install_galaxy --galaxy_branch "dev"
 #abims_CAMERA_annotateDiffreport[0]: passed
 
 
+# -- Use of conda dependencies
+planemo conda_init --conda_prefix /tmp/mc
+planemo conda_install --conda_prefix /tmp/mc . 
+planemo test --install_galaxy --conda_prefix /tmp/mc --conda_dependency_resolution --galaxy_branch "dev"
+
+#All 1 test(s) executed passed.
+#abims_CAMERA_annotateDiffreport[0]: passed
+
+
+# -- Use of shed_test
 planemo shed_test --install_galaxy -t testtoolshed --galaxy_branch "dev"
 
 #All 1 test(s) executed passed.

galaxy/camera_combinexsannos/abims_CAMERA_combinexsAnnos.xml

@@ -47,12 +47,12 @@
     <tests>
         <test>
             <!-- TODO: generer des vrais dataset pos et neg-->
-            <param name="image_pos" value="xset.group.retcor.group.fillPeaks.annotate.positive.Rdata"/>
-            <param name="image_neg" value="xset.group.retcor.group.fillPeaks.annotate.negative.Rdata"/>
+            <param name="image_pos" value="faahOK.xset.group.retcor.group.fillPeaks.annotate.positive.Rdata"/>
+            <param name="image_neg" value="faahOK.xset.group.retcor.group.fillPeaks.annotate.negative.Rdata"/>
             <param name="pos" value="TRUE"/>
             <param name="tol" value="2"/>
             <param name="ruleset" value="1,1"/>
-            <output name="variableMetadata" file="xset.group.retcor.group.fillPeaks.annotate.positive.combinexsAnnos.variableMetadata.tsv" />
+            <output name="variableMetadata" file="faahOK.xset.group.retcor.group.fillPeaks.annotate.positive.combinexsAnnos.variableMetadata.tsv" />
         </test>
     </tests>
 

galaxy/camera_combinexsannos/planemo_test.sh

@@ -0,0 +1,19 @@
+# Example of planemo command to launch test
+
+# Note: --galaxy_branch "dev" is set to deal with zip file
+
+
+# -- Use of conda dependencies
+planemo conda_init --conda_prefix /tmp/mc
+planemo conda_install --conda_prefix /tmp/mc . 
+planemo test --install_galaxy --conda_prefix /tmp/mc --conda_dependency_resolution --galaxy_branch "dev"
+
+#All 1 test(s) executed passed.
+#abims_CAMERA_combinexsAnnos[0]: passed
+
+
+# -- Use of shed_test
+planemo shed_test --install_galaxy -t testtoolshed
+
+#All 1 test(s) executed passed.
+#testtoolshed.g2.bx.psu.edu/repos/mmonsoor/camera_combinexsannos/abims_CAMERA_combinexsAnnos/2.0.4[0]: passed

galaxy/camera_combinexsannos/tool_test_output.json

@@ -0,0 +1 @@
+{"tests": [{"data": {"status": "success", "inputs": {"image_neg": {"src": "hda", "id": "5729865256bc2525"}, "image_pos": {"src": "hda", "id": "2891970512fa2d5a"}, "pos": "TRUE", "tol": "2", "ruleset": "1,1"}, "job": {"inputs": {"image_neg": {"src": "hda", "id": "5729865256bc2525", "uuid": "6d80778d-9a1b-4c0a-bc36-1b4eeaf65446"}, "image_pos": {"src": "hda", "id": "2891970512fa2d5a", "uuid": "79b78f62-7b98-4bd6-a6a0-7d4ab741aef5"}}, "update_time": "2016-04-25T14:03:29.463841", "tool_id": "testtoolshed.g2.bx.psu.edu/repos/mmonsoor/camera_combinexsannos/abims_CAMERA_combinexsAnnos/2.0.4", "outputs": {"variableMetadata": {"src": "hda", "id": "54f2a3a23292eb07", "uuid": "c57ee027-b0c1-4998-a0eb-40d43e070ade"}}, "stdout": "\tPACKAGE INFO\nparallel\t3.1.2\nBiocGenerics\t0.14.0\nBiobase\t2.28.0\nRcpp\t0.12.0\nmzR\t2.2.2\nxcms\t1.44.0\nsnow\t0.3.13\nigraph\t0.7.1\nCAMERA\t1.26.0\nmulttest\t2.22.0\nbatch\t1.1.4\n\n\n\tARGUMENTS INFO\nxfunction\tcombinexsAnnos\nimage_pos\t/tmp/tmpAwoHl7/files/000/dataset_1.dat\nimage_neg\t/tmp/tmpAwoHl7/files/000/dataset_2.dat\nvariableMetadataOutput\t/tmp/tmpAwoHl7/files/000/dataset_3.dat\npos\tTRUE\ntol\t2\nruleset\t1,1\nconvert_param\tFALSE\nkeep_meta\tTRUE\n\n\n\tINFILE PROCESSING INFO\n\n\n\tARGUMENTS PROCESSING INFO\n\n\n\tMAIN PROCESSING INFO\n\tObject xset from positive mode\nAn \"xsAnnotate\" object!\nWith 6245 groups (pseudospectra)\nWith 4 samples and 8157 peaks\nPolarity mode is set to:  positive \nUsing automatic sample selection\nAnnotated isotopes: 209 \nAnnotated adducts & fragments: 584 \nMemory usage: 7.08 MB\n\n\tObject xset from negative mode\nAn \"xsAnnotate\" object!\nWith 6245 groups (pseudospectra)\nWith 4 samples and 8157 peaks\nPolarity mode is set to:  negative \nUsing automatic sample selection\nAnnotated isotopes: 209 \nAnnotated adducts & fragments: 451 \nMemory usage: 6.84 MB\n\n\n\tCombining...\nRun combining of xsAnnotates\n % finished: 10  20  30  40  50  60  70  80  90  100  \nGenerate Peaklist....\nnull device \n          1 \n\n\n\tDONE\n", "command_line": "LANG=C Rscript /tmp/tmpAwoHl7/shed_tools/testtoolshed.g2.bx.psu.edu/repos/mmonsoor/camera_combinexsannos/9a1a72ee9418/camera_combinexsannos/CAMERA.r  xfunction combinexsAnnos image_pos /tmp/tmpAwoHl7/files/000/dataset_1.dat image_neg /tmp/tmpAwoHl7/files/000/dataset_2.dat  variableMetadataOutput /tmp/tmpAwoHl7/files/000/dataset_3.dat  pos TRUE tol 2 ruleset 1,1 convert_param FALSE keep_meta TRUE", "exit_code": 0, "state": "ok", "create_time": "2016-04-25T14:01:03.733543", "params": {"tol": "\"2\"", "pos": "\"TRUE\"", "dbkey": "\"hg17\"", "keep_meta": "\"True\"", "ruleset": "\"1,1\"", "convert_param": "\"False\"", "chromInfo": "\"/tmp/tmpAwoHl7/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "", "job_metrics": [], "model_class": "Job", "external_id": "81656", "id": "54f2a3a23292eb07", "user_email": "[email protected]"}}, "id": "functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/mmonsoor/camera_combinexsannos/abims_CAMERA_combinexsAnnos/2.0.4.test_tool_000000", "has_data": true}], "version": "0.1", "exit_code": 0, "summary": {"num_skips": 0, "num_errors": 0, "num_failures": 0, "num_tests": 1}}

galaxy/camera_suite/test-data/faahOK.xset.group.retcor.group.fillPeaks.annotate.negative.Rdata

@@ -0,0 +1 @@
+../../camera_combinexsannos/test-data/faahOK.xset.group.retcor.group.fillPeaks.annotate.negative.Rdata

galaxy/camera_suite/test-data/faahOK.xset.group.retcor.group.fillPeaks.annotate.positive.Rdata

@@ -0,0 +1 @@
+../../camera_combinexsannos/test-data/faahOK.xset.group.retcor.group.fillPeaks.annotate.positive.Rdata

galaxy/camera_suite/test-data/faahOK.xset.group.retcor.group.fillPeaks.annotate.positive.combinexsAnnos.variableMetadata.tsv

@@ -0,0 +1 @@
+../../camera_combinexsannos/test-data/faahOK.xset.group.retcor.group.fillPeaks.annotate.positive.combinexsAnnos.variableMetadata.tsv

src/camera_w4m_script/CAMERA.r

@@ -39,14 +39,16 @@ if (!is.null(listArguments[["image"]])){
 
 if (listArguments[["xfunction"]] %in% c("combinexsAnnos")) {
   load(listArguments[["image_pos"]])
-  xaP=xa  
+  xaP=xa
+  listOFlistArgumentsP=listOFlistArguments
   if (exists("xsAnnotate_object")) xaP=xsAnnotate_object
 
   diffrepP=NULL
   if (exists("diffrep")) diffrepP=diffrep
 
   load(listArguments[["image_neg"]])
   xaN=xa
+  listOFlistArgumentsN=listOFlistArguments
   if (exists("xsAnnotate_object")) xaN=xsAnnotate_object
 
   diffrepN=NULL
@@ -158,7 +160,7 @@ if (thefunction %in% c("annotatediff")) {
 }
 
 if (thefunction %in% c("combinexsAnnos")) {
-  cAnnot=combinexsAnnos_function(xaP=xaP,xaN=xaN,diffrepP=diffrepP,diffrepN=diffrepN,convert_param=listArguments[["convert_param"]],pos=listArguments[["pos"]],tol=listArguments[["tol"]],ruleset=listArguments[["ruleset"]],keep_meta=listArguments[["keep_meta"]],variableMetadataOutput=variableMetadataOutput)
+  cAnnot=combinexsAnnos_function(xaP=xaP,xaN=xaN,listOFlistArgumentsP=listOFlistArgumentsP,listOFlistArgumentsN=listOFlistArgumentsN,diffrepP=diffrepP,diffrepN=diffrepN,convert_param=listArguments[["convert_param"]],pos=listArguments[["pos"]],tol=listArguments[["tol"]],ruleset=listArguments[["ruleset"]],keep_meta=listArguments[["keep_meta"]],variableMetadataOutput=variableMetadataOutput)
 }
 
 dev.off()

src/camera_w4m_script/lib.r

@@ -114,7 +114,7 @@ annotatediff <- function(xset=xset, listArguments=listArguments, variableMetadat
 }
 
 
-combinexsAnnos_function <- function(xaP, xaN, diffrepP=NULL,diffrepN=NULL,convert_param=FALSE,pos=TRUE,tol=2,ruleset=NULL,keep_meta=TRUE, variableMetadataOutput="variableMetadata.tsv"){
+combinexsAnnos_function <- function(xaP, xaN, listOFlistArgumentsP,listOFlistArgumentsN, diffrepP=NULL,diffrepN=NULL,convert_param=FALSE,pos=TRUE,tol=2,ruleset=NULL,keep_meta=TRUE, variableMetadataOutput="variableMetadata.tsv"){
 
   #Load the two Rdata to extract the xset objects from positive and negative mode
   cat("\tObject xset from positive mode\n")
@@ -143,12 +143,15 @@ combinexsAnnos_function <- function(xaP, xaN, diffrepP=NULL,diffrepN=NULL,conver
 
   if(pos){
     xa=xaP
+    listOFlistArgumentsP=listOFlistArguments
     mode="neg. Mode"
   } else {
     xa=xaN
+    listOFlistArgumentsN=listOFlistArguments
     mode="pos. Mode"
   }
-  peakList=getPeaklist(xa,intval=listArguments[["intval"]])
+  intval = "into"; for (steps in names(listOFlistArguments)) { if (!is.null(listOFlistArguments[[steps]]$intval)) intval = listOFlistArguments[[steps]]$intval }
+  peakList=getPeaklist(xa,intval=intval)
   peakList=cbind(groupnames(xa@xcmsSet),peakList); colnames(peakList)[1] = c("name");
   variableMetadata=cbind(peakList, cAnnot[, c("isotopes", "adduct", "pcgroup",mode)]);
   variableMetadata=variableMetadata[,!(colnames(variableMetadata) %in% c(sampnames(xa@xcmsSet)))]