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changeset 1:7f5bf24d5aeb draft

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"planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/autospill commit 8fafcaef24d23a785759004c5794a9cae485dfb1"
author azomics
date Sat, 19 Jun 2021 10:57:45 +0000
parents 315be37a7ac9
children 3293c160f73c
files autospill.xml test-data/Compensation Controls_FITC Stained Control_001.fcs test-data/Compensation Controls_PE-CF594 Stained Control_025.fcs test-data/Compensation Controls_PE-Cy5.5 Stained Control_027.fcs test-data/fcs_control.csv
diffstat 5 files changed, 20 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/autospill.xml	Tue May 25 00:07:20 2021 +0000
+++ b/autospill.xml	Sat Jun 19 10:57:45 2021 +0000
@@ -1,9 +1,9 @@
-<tool id="autospill" name="Autospill" version="0.1.0+galaxy0" profile="19.01" python_template_version="3.5">
+<tool id="autospill" name="Autospill" version="0.2.0+galaxy0" profile="19.01" python_template_version="3.5">
     <description>
       calculates spillover coefficients with robust linear models and then refines spillover coefficients iteratively
     </description>
     <requirements>
-      <requirement type="package" version="0.1.0">r-autospill</requirement>
+      <requirement type="package" version="0.2.0">r-autospill</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
       mkdir input_dir;
@@ -205,6 +205,20 @@
         <discover_datasets pattern="__designation_and_ext__" format="png" directory="figure_compensation" visible="true" />
       </collection> -->
     </outputs>
+    <tests>
+      <test>
+        <param name="fcs_list" value="Compensation Controls_FITC Stained Control_001.fcs,Compensation Controls_PE-CF594 Stained Control_025.fcs,Compensation Controls_PE-Cy5.5 Stained Control_027.fcs"/>
+        <param name="fcs_metadata" value="fcs_control.csv" ftype="csv"/>
+        <param name="get_figure_scatter" value="false"/>
+        <param name="get_error" value="false"/>
+        <param name="get_gates" value="false"/>
+        <output name="spillover_matrix">
+          <assert_contents>
+            <has_n_lines n="4" />
+          </assert_contents>
+        </output>
+      </test>
+    </tests>
     <help><![CDATA[
 Autospill: a principled framework that simplifies the analysis of multichromatic flow cytometry data
 ----------------------------------------------------------------------------------------------------
Binary file test-data/Compensation Controls_FITC Stained Control_001.fcs has changed
Binary file test-data/Compensation Controls_PE-CF594 Stained Control_025.fcs has changed
Binary file test-data/Compensation Controls_PE-Cy5.5 Stained Control_027.fcs has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fcs_control.csv	Sat Jun 19 10:57:45 2021 +0000
@@ -0,0 +1,4 @@
+filename,dye,antigen,wavelength
+Compensation Controls_FITC Stained Control_001.fcs,FITC-A,CD3/CD4/TCRb,525
+Compensation Controls_PE-CF594 Stained Control_025.fcs,PE-CF594-A,CD4,612
+Compensation Controls_PE-Cy5.5 Stained Control_027.fcs,PE-Cy5.5-A,CD3,678