Mercurial > repos > azomics > flow_compensate

comparison flow-compensate.xml @ 1:ffc083c86d44 draft default tip

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"planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit fd7533e2c5c6c078bd2734c1ded95db9b74e450e"
author azomics
date Wed, 23 Jun 2021 21:56:39 +0000
parents ca7ba337b727
children
comparison
equal deleted inserted replaced
0:ca7ba337b727 1:ffc083c86d44
9 mkdir -p input_dir; 9 mkdir -p input_dir;
10 #for $fcs in $fcs_list: 10 #for $fcs in $fcs_list:
11 ln -s '$fcs' input_dir/'$fcs.element_identifier'; 11 ln -s '$fcs' input_dir/'$fcs.element_identifier';
12 #end for 12 #end for
13 mkdir -p output_dir; 13 mkdir -p output_dir;
14 Rscript '$compensate_script' '$compensation_matrix' input_dir output_dir 14 Rscript '$compensate_script' '$compensation_matrix' input_dir output_dir &> '$log_file'
15 ]]></command> 15 ]]></command>
16 <configfiles> 16 <configfiles>
17 <configfile name="compensate_script"><![CDATA[ 17 <configfile name="compensate_script"><![CDATA[
18 library(flowCore) 18 library(flowCore)
19 19
45 </inputs> 45 </inputs>
46 <outputs> 46 <outputs>
47 <collection name="compensated_fcs" format="fcs" label="${tool.name} compensated FCS files on ${on_string}" type="list"> 47 <collection name="compensated_fcs" format="fcs" label="${tool.name} compensated FCS files on ${on_string}" type="list">
48 <discover_datasets pattern="__designation_and_ext__" directory="output_dir" visible="true" /> 48 <discover_datasets pattern="__designation_and_ext__" directory="output_dir" visible="true" />
49 </collection> 49 </collection>
50 <data name="log_file" format="txt" label="Log for compensation by ${tool.name} on ${on_string}"/>
50 </outputs> 51 </outputs>
51 <help><![CDATA[ 52 <help><![CDATA[
52 TODO: Fill in help. 53 TODO: Fill in help.
53 ]]></help> 54 ]]></help>
54 </tool> 55 </tool>