diff scanpy-normalise-data.xml @ 6:9e42d8795385 draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 400799f99ee36ad12b990b1ccabf4be16a26c003

--- a/scanpy-normalise-data.xml	Wed Nov 20 05:11:20 2019 -0500
+++ b/scanpy-normalise-data.xml	Mon Nov 25 14:36:21 2019 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_normalise_data" name="Scanpy NormaliseData" version="@TOOL_VERSION@+galaxy3">
+<tool id="scanpy_normalise_data" name="Scanpy NormaliseData" version="@TOOL_VERSION@+galaxy6">
   <description>to make all cells having the same total expression</description>
   <macros>
     <import>scanpy_macros2.xml</import>
@@ -25,7 +25,7 @@
     <param name="fraction" argument="--fraction" type="float" value="1" min="0" max="1"
            label="Exclude top expressed genes until the remaining account for no greater than specified fraction of total counts"
            help="Only non-excluded genes will sum up the target number."/>
-    <param name="log_transform" argument="--no-log-transform" type="boolean" truevalue="" falsevalue="--no-log-transform" checked="True" 
+    <param name="log_transform" argument="--no-log-transform" type="boolean" truevalue="" falsevalue="--no-log-transform" checked="True"
            label="Apply log transform?" help="If enabled, will apply a log transformation following normalisation."/>
     <param name="save_raw" argument="--save-raw" type="boolean" truevalue="yes" falsevalue="no" checked="true"
            label="Save normalised data in `.raw`" help="The saved normalised data are log1p transformed."/>
@@ -33,7 +33,7 @@
   </inputs>
 
   <outputs>
-    <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Normalised data"/>
+    <expand macro="output_data_obj" description="Normalised data"/>
     <expand macro="export_mtx_outputs"/>
   </outputs>