v2.0.0+galaxy1 (#13)

* Add GALAXY_SLOTS variable
* Add block_size parameter for 'align samples' tool

Author: RJMW

tools/dimspy/align_samples.xml

@@ -1,4 +1,4 @@
-<tool id="dimspy_align_samples" name="Align Samples" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
+<tool id="dimspy_align_samples" name="Align Samples" version="@TOOL_VERSION@+galaxy1">
     <description> - Align peaks across Peaklists</description>
     <macros>
         <import>macros.xml</import>
@@ -13,6 +13,8 @@
             --filelist '$filelist'
         #end if
         --ppm $ppm
+        --ncpu \${GALAXY_SLOTS:-1}
+        --block-size $adv.block_size
         #if $hdf5_to_txt.standard
             &&
             @HDF5_PM_TO_TXT@
@@ -29,6 +31,9 @@
         <param name="ppm" argument="--ppm" type="float" value="2.0" label="Ppm error tolerance" help="Maximum tolerated m/z deviation across samples in parts per million (ppm)." />
         <param name="delimiter" argument="--delimiter" type="hidden" value="tab" />
         <expand macro="hdf5_pm_to_txt" />
+        <section name="adv" title="Advanced options" expanded="False">
+            <param name="block_size" argument="--block-size" type="integer" value="5000" label="Block size" help="The size of each block of peaks to perform clustering on." />
+        </section>
     </inputs>
     <outputs>
         <expand macro="outputs_peak_intensity_matrix" />
@@ -47,6 +52,22 @@
             <output name="hdf5_file_out" file="pm_as.h5" ftype="h5" compare="sim_size"/>
             <output name="matrix_file_out" file="peak_matrix_as.txt" ftype="tsv"/>
         </test>
+        <test>
+            <param name="hdf5_file_in" value="pls_rf.h5" ftype="h5"/>
+            <param name="ppm" value="2.0"/>
+            <param name="delimiter" value="tab"/>
+            <conditional name="hdf5_to_txt" >
+                <param name="standard" value="True"/>
+                <param name="comprehensive" value="False"/>
+                <param name="samples_representations" value="rows"/>
+                <param name="matrix_attr" value="intensity"/>
+            </conditional>
+            <section name="adv">
+                <param name="block_size" value="10000"/>
+            </section>
+            <output name="hdf5_file_out" file="pm_as.h5" ftype="h5" compare="sim_size"/>
+            <output name="matrix_file_out" file="peak_matrix_as.txt" ftype="tsv"/>
+        </test>
         <test>
             <param name="hdf5_file_in" value="pls_rf.h5" ftype="h5"/>
             <param name="ppm" value="2.0"/>

tools/dimspy/process_scans.xml

@@ -1,4 +1,4 @@
-<tool id="dimspy_process_scans" name="Process Scans (and SIM-Stitch)" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
+<tool id="dimspy_process_scans" name="Process Scans (and SIM-Stitch)" version="@TOOL_VERSION@+galaxy1">
     <description> - Read, filter and average MS scans</description>
     <macros>
         <import>macros.xml</import>
@@ -56,6 +56,7 @@
             #end for
         #end if
         --report '$report'
+        --ncpu \${GALAXY_SLOTS:-1}
         &&
         dimspy hdf5-pls-to-txt
         --input '$hdf5_file_out'

tools/dimspy/replicate_filter.xml

@@ -1,4 +1,4 @@
-<tool id="dimspy_replicate_filter" name="Replicate Filter" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
+<tool id="dimspy_replicate_filter" name="Replicate Filter" version="@TOOL_VERSION@+galaxy1">
     <description> - Remove peaks that fail to appear in at least x-out-of-n (technical) replicates</description>  
     <macros>
         <import>macros.xml</import>
@@ -19,6 +19,7 @@
             --rsd-threshold $rsd_threshold
         #end if
         --report '$report'
+        --ncpu \${GALAXY_SLOTS:-1}
         &&
         dimspy create-sample-list
         --input '$hdf5_file_out'