changeset 0:4082283be00c draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/2018_07_mz_hdf5_to_dat.xml	Mon Apr 26 14:53:35 2021 +0000
@@ -0,0 +1,114 @@
+<tool id="2021_05_hdf5_to_dat" name="MS .h5 -> MS .dat " version="0.0.1">
+
+<description> from an Orbitrap MS  </description>
+ 
+
+<requirements>
+    <requirement type="package" >scilab</requirement>
+  </requirements>
+
+
+<stdio>
+    <exit_code range="1:" level="fatal" />
+</stdio>
+
+
+<command> <![CDATA[
+   if [ -d $__root_dir__/packages/scilab-6.1.0 ]; then $__root_dir__/packages/scilab-6.1.0/bin/scilab-cli -nb -quit -f $* < ${script_file}; else scilab-cli -nb -quit -f $* < ${script_file}; fi
+]]>
+</command>
+
+
+  <configfiles>
+    <configfile name="script_file">
+        <![CDATA[ exec("$__tool_directory__/src/mz_hdf5tosci.sci",-1); ...
+        if ~isdef('pls') then ...
+           atomsSystemUpdate(); ...
+           atomsInstall('FACT'); ...
+           atomsLoad('FACT'); ...
+        end; ...
+        lasterror(); ...
+        res=mz_hdf5tosci("${filein}"); ...
+        save("${res}",'res'); ...
+        if ~isempty(lasterror(%f)) then ...
+        write(0,lasterror()); ...
+        end ]]>
+    </configfile>
+  </configfiles>
+
+
+  <inputs>
+     <param name="filein"       format="h5"                type="data"      label="Mass spectrum, .h5 format"    />
+  </inputs>
+  
+
+  <outputs>
+      
+      <data name="res"      format="mat"             label="${filein.name}.dat"  />
+    
+  </outputs>
+ 
+ 
+  <tests>
+    <test>
+       <param name="filein" value="VI2016_AC_4Areduit_1.h5"/>
+       <output name="res"   file="VI2016_AC_4Areduit_1.dat" compare="sim_size" delta="500" />
+    </test>
+  </tests>
+
+ <help>
+
+
+**Author**  Jean-Claude Boulet (INRAE).
+
+
+---------------------------------------------------
+
+=================
+MS .h5 -> MS .dat
+=================
+
+-----------
+Description
+-----------
+
+This function converts an Orbitrap HDF5 mass spectrum into a Scilab mass spectrum
+
+-----
+Input
+-----
+
+**an .h5 hrms**
+
+Previously, Orbitrap devices yielded .raw files.
+
+MSconvert selected MS1 and performed the conversion .raw -> .md5 
+
+Then HDF5View performed the conversion .md5 -> .h5 
+which is the format of the input file.
+
+
+-------
+Outputs
+-------
+
+**a .dat mass spectrum**
+
+This is an HDF5 file whose structure is specific to Scilab.
+
+It contains two fields:
+
+- time: the retention times, a vector;
+
+- mzdata: a list containing a MS1 spectrum (m/z + signals) for each retention time.
+
+
+</help>
+
+<citations> 
+
+</citations>
+
+
+
+</tool>