Mercurial > repos > lecorguille > camera_annotate

changeset 8:8c5bb7b86df9 draft

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planemo upload
author lecorguille
date Mon, 22 Feb 2016 16:48:11 -0500
parents 9882346d42a8
children 7da9252dd983
files Makefile README.rst abims_CAMERA_annotateDiffreport.xml tool_dependencies.xml
diffstat 4 files changed, 109 insertions(+), 25 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Makefile	Mon Feb 22 16:48:11 2016 -0500
@@ -0,0 +1,23 @@
+# USAGE: make [install|clean]
+
+# -------- VARIABLE --------
+
+OBJ=camera_annotate.tgz
+DEP=abims_CAMERA_annotateDiffreport.xml tool_dependencies.xml repository_dependencies.xml static test-data
+
+
+# ------------------------
+
+all: $(OBJ)
+
+$(OBJ): $(DEP)
+	tar --exclude=".svn" -zchf $@ $^
+
+# ------------------------
+
+install: $(OBJ)
+	mv *.tgz ~
+
+clean:
+	rm *.tgz
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Mon Feb 22 16:48:11 2016 -0500
@@ -0,0 +1,29 @@
+
+Changelog/News
+--------------
+
+**Version  2.1.3 - 10/02/2016**
+
+- BUGFIX: better management of errors. Datasets remained green although the process failed
+
+- BUGFIX: the conversion into minutes of the retention time was applied to the diffreport outputs (several conditions)
+
+- IMPROVEMENT: when there are several conditions, the tool will generate individual datasets (tsv, pdf) instead of a zip file. The usual png (eic, boxplot) will from now be integrated in two pdf.
+
+- UPDATE: refactoring of internal management of inputs/outputs
+
+
+VERSION 2.1.0 - 09/10/2015**
+
+- BUGFIX: There was a bug with the CAMERA.annotate (generating a bad dataMatrix (intensities which don't match with the metabolites))
+
+
+VERSION 2.1.0 - 07/06/2015**
+
+- IMPROVEMENT: new datatype/dataset formats (rdata.camera.positive, rdata.camera.negative, rdata.camera.quick ...) will facilitate the sequence of tools and so avoid incompatibility errors.
+
+- IMPROVEMENT: parameter labels have changed to facilitate their reading.
+
+- UPDATE: merged with annotateDiffreport. Some parameters are dedicated to experiences with several conditions
+
+
--- a/abims_CAMERA_annotateDiffreport.xml	Thu Dec 17 09:09:41 2015 -0500
+++ b/abims_CAMERA_annotateDiffreport.xml	Mon Feb 22 16:48:11 2016 -0500
@@ -1,4 +1,4 @@
-<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.1.0">
+<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.1.3">
 
     <description>CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition.</description>
     
@@ -7,17 +7,27 @@
         <requirement type="binary">Rscript</requirement>
         <requirement type="package" version="1.44.0">xcms</requirement>
         <requirement type="package" version="1.22.0">camera</requirement>
-        <requirement type="package" version="2.1">camera_w4m_script</requirement>
+        <requirement type="package" version="2.2.1">camera_w4m_script</requirement>
+        <requirement type="binary">CAMERA.r</requirement>
+        <requirement type="package" version="1.3.18">graphicsmagick</requirement>
+        <requirement type="binary">convert</requirement>
     </requirements>
     
     <stdio>
         <exit_code range="1:" level="fatal" />
     </stdio>
 
-    <command interpreter="Rscript">
+    <command><![CDATA[
         CAMERA.r 
-        xfunction annotatediff image $image
-        convert_param $convert_param num_digits $num_digits nSlaves \${GALAXY_SLOTS:-1}
+        xfunction annotatediff 
+        image $image
+
+        variableMetadataOutput $variableMetadata
+        dataMatrixOutput $datamatrix
+        xsetRdataOutput $rdata
+
+        convert_param $convert_param num_digits $num_digits 
+        nSlaves \${GALAXY_SLOTS:-1}
         sigma $sigma perfwhm $perfwhm 
         maxcharge $maxcharge maxiso $maxiso minfrac $minfrac
         ppm $ppm mzabs $mzabs intval $intval 
@@ -35,6 +45,7 @@
         #end if
 
         #if $options.option == "show":
+            runDiffreport TRUE
             eicmax $options.eicmax
             eicwidth $options.eicwidth
             value $options.value
@@ -42,24 +53,11 @@
             h $options.h
             w $options.w
             mzdec $options.mzdec
-        #else
-            eicmax 0
-            eicwidth 200
-            value "into"
-            sortpval TRUE 
-            h 480
-            w 640
-            mzdec 2
+            new_file_path ${__new_file_path__}/primary_${output_diffreport.id}_
         #end if
-        &amp;&amp; (
-            mv variableMetadata.tsv $variableMetadata;
-            mv dataMatrix.tsv $datamatrix;
-            mv annotatediff.RData $rdata
-        );
-        cat xset.log
         
       
-    </command>
+    ]]></command>
 
     <inputs>
     
@@ -145,7 +143,7 @@
                 <when input="quick_block.polarity" value="negative" format="rdata.camera.negative" />
             </change_format>
         </data>
-	<data name="output_zip" format="zip" from_work_dir="Xdiffreport.zip" label="${image.name[:-6]}.annotateDiffreport.zip" >
+	<data name="output_diffreport" format="text" label="${image.name[:-6]}.annotateDiffreport" hidden="True">
 		 <filter>(options['option'] == 'show')</filter>
 	</data>    
     </outputs>
@@ -189,7 +187,7 @@
     
     
     
-    <help>
+    <help><![CDATA[
         
 .. class:: infomark
 
@@ -374,7 +372,38 @@
 
 .. image:: annotatediffreport_variableMetadata.png
 
-    </help>
+
+---------------------------------------------------
+
+Changelog/News
+--------------
+
+**Version  2.1.3 - 10/02/2016**
+
+- BUGFIX: better management of errors. Datasets remained green although the process failed
+
+- BUGFIX: the conversion into minutes of the retention time was applied to the diffreport outputs (several conditions)
+
+- IMPROVEMENT: when there are several conditions, the tool will generate individual datasets (tsv, pdf) instead of a zip file. The usual png (eic, boxplot) will from now be integrated in two pdf.
+
+- UPDATE: refactoring of internal management of inputs/outputs
+
+
+VERSION 2.1.0 - 09/10/2015**
+
+- BUGFIX: There was a bug with the CAMERA.annotate (generating a bad dataMatrix (intensities which don't match with the metabolites))
+
+
+VERSION 2.1.0 - 07/06/2015**
+
+- IMPROVEMENT: new datatype/dataset formats (rdata.camera.positive, rdata.camera.negative, rdata.camera.quick ...) will facilitate the sequence of tools and so avoid incompatibility errors.
+
+- IMPROVEMENT: parameter labels have changed to facilitate their reading.
+
+- UPDATE: merged with annotateDiffreport. Some parameters are dedicated to experiences with several conditions
+
+
+    ]]></help>
 
     <citations>
         <citation type="doi">10.1021/ac202450g</citation>
--- a/tool_dependencies.xml	Thu Dec 17 09:09:41 2015 -0500
+++ b/tool_dependencies.xml	Mon Feb 22 16:48:11 2016 -0500
@@ -6,7 +6,10 @@
     <package name="camera" version="1.22.0">
         <repository changeset_revision="845eb883bd1b" name="package_r_camera_1_22_0" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
-    <package name="camera_w4m_script" version="2.1">
-        <repository changeset_revision="208bc3eea24c" name="package_camera_w4m_script_2_1" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="camera_w4m_script" version="2.2.1">
+        <repository changeset_revision="91b0d23c9d52" name="package_camera_w4m_script_2_2_1" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="graphicsmagick" version="1.3.18">
+        <repository changeset_revision="ef238a8bdc1d" name="package_graphicsmagick_1_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>