Mercurial > repos > computational-metabolomics > dimspy_align_samples

changeset 2:7b6f148bd99f draft default tip

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"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 80069808371b58f45da0c8133c27d67ac1a5b448"
author computational-metabolomics
date Wed, 17 Feb 2021 10:57:52 +0000
parents c72868b80c29
children
files README.rst align_samples.xml
diffstat 2 files changed, 28 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/README.rst	Tue Apr 28 17:44:59 2020 -0400
+++ b/README.rst	Wed Feb 17 10:57:52 2021 +0000
@@ -1,6 +1,6 @@
 Galaxy tool wrappers for DIMSpy
 ===============================
-|Build Status (Travis)| |galaxy-eu| |Git| |Bioconda| |License|
+|Build Status (last commit)| |Build Status (weekly global test)| |galaxy-eu| |Git| |Bioconda| |License|
 
 Galaxy tool wrappers for Python package DIMSpy: data processing of direct-infusion mass spectrometry (DIMS)-based metabolomics and lipidomics data
 
@@ -63,8 +63,11 @@
 section 3.3 of the RawFileReader License, and is not granted rights to redistribute RawFileReader.
 
 
-.. |Build Status (Travis)| image:: https://img.shields.io/travis/computational-metabolomics/dimspy-galaxy.svg?style=flat&maxAge=3600&label=Travis-CI
-   :target: https://travis-ci.com/computational-metabolomics/dimspy-galaxy
+.. |Build Status (last commit)| image:: https://github.com/computational-metabolomics/dimspy-galaxy/workflows/Galaxy%20Tool%20Linting%20and%20Tests%20for%20push%20and%20PR/badge.svg
+   :target: https://github.com/computational-metabolomics/dimspy-galaxy/actions?query=workflow%3A%22Galaxy+Tool+Linting+and+Tests+for+push+and+PR%22
+
+.. |Build Status (weekly global test)| image:: https://github.com/computational-metabolomics/dimspy-galaxy/workflows/Weekly%20global%20Tool%20Linting%20and%20Tests/badge.svg
+   :target: https://github.com/computational-metabolomics/dimspy-galaxy/actions?query=workflow%3A%22Weekly+global+Tool+Linting+and+Tests%22
 
 .. |Git| image:: https://img.shields.io/badge/repository-GitHub-blue.svg?style=flat&maxAge=3600
    :target: https://github.com/computational-metabolomics/dimspy
--- a/align_samples.xml	Tue Apr 28 17:44:59 2020 -0400
+++ b/align_samples.xml	Wed Feb 17 10:57:52 2021 +0000
@@ -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" />
@@ -51,6 +56,22 @@
             <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"/>
+            <param name="delimiter" value="tab"/>
             <conditional name="hdf5_to_txt">
                 <param name="standard" value="True"/>
                 <param name="comprehensive" value="False"/>