# HG changeset patch
# User tomnl
# Date 1522418831 14400
# Node ID 2365c3b350fa4153800c5c678f05ee9b587567d9
# Parent  db98e5d3595a3bad457e1ef90a2c73a9b398ad73
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty

diff -r db98e5d3595a -r 2365c3b350fa frag4feature.R
--- a/frag4feature.R	Tue Mar 27 12:29:51 2018 -0400
+++ b/frag4feature.R	Fri Mar 30 10:07:11 2018 -0400
@@ -19,13 +19,15 @@
 
     nsave <- names(pa@fileList)
     old_filenames  <- basename(pa@fileList)
+ 
     pa@fileList <- filepaths[match(names(pa@fileList), galaxy_names)]
     names(pa@fileList) <- nsave
 
     pa@puritydf$filename <- basename(pa@fileList[match(pa@puritydf$filename, old_filenames)])
     pa@grped_df$filename <- basename(pa@fileList[match(pa@grped_df$filename, old_filenames)])
   }
-
+ print(pa@fileList)
+ print(xset@filepaths)
 
  if(!all(basename(pa@fileList)==basename(xset@filepaths))){
     if(!all(names(pa@fileList)==basename(xset@filepaths))){
diff -r db98e5d3595a -r 2365c3b350fa frag4feature.xml
--- a/frag4feature.xml	Tue Mar 27 12:29:51 2018 -0400
+++ b/frag4feature.xml	Fri Mar 30 10:07:11 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="frag4feature" name="frag4feature" version="0.0.15">
+<tool id="frag4feature" name="frag4feature" version="0.0.17">
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -52,7 +52,7 @@
     <inputs>
 
         <param type="data" name="xset" label="xcmsSet object"
-               help="xcmsSet object saved as 'xset' in an RData file" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata.camera.quick,rdata.camera.positive,rdata.camera.negative,rdata"/>
+               help="grouped xcmsSet object saved as 'xset' in an RData file" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata.camera.quick,rdata.camera.positive,rdata.camera.negative,rdata"/>
         <param type="data" name="pa" label="purityA object" format="rdata"
                help="purityA object saved as 'pa' in a RData file (output from assess_purity_msms)"/>
 
@@ -111,7 +111,9 @@
 Description
 -----------
 
-Tool to link XCMS features to fragmentation spectra and create an SQLite database of all the data and connections.
+Tool to link XCMS features to fragmentation spectra and create an SQLite database of all the data and connections. 
+
+Please note that the xcmsSet object needs to have been grouped.
 
 The data inputs are:
 
@@ -119,7 +121,7 @@
 * A xcmsSet grouped object (generated from xcms_group) saved in an rdata file
 * [optional] a dataset collection of the mzML files to resubmit
 
-See Bioconductor documentation for more details, function msPurity::dimsPredictPurity()
+See Bioconductor documentation for more details, function msPurity::frag4feature()
 
 -----------
 Outputs
diff -r db98e5d3595a -r 2365c3b350fa macros.xml
--- a/macros.xml	Tue Mar 27 12:29:51 2018 -0400
+++ b/macros.xml	Fri Mar 30 10:07:11 2018 -0400
@@ -2,7 +2,7 @@
 <macros>
     <xml name="requirements">
         <requirements>
-           <requirement type="package" version="1.5.2" >bioconductor-mspurity</requirement>
+           <requirement type="package" version="1.5.4" >bioconductor-mspurity</requirement>
            <requirement type="package" version="1.4.4" >r-optparse</requirement>
             <yield />
         </requirements>