Commit 44dfe31e authored by Yakubov, Sergey's avatar Yakubov, Sergey
Browse files

Merge branch '108-update-export-tool-to-export-multiple-collection' into 'dev' 

update export tool to support multiple collections

Closes #108

See merge request ndip/galaxy-tools!182
parents 305bfa10 648836ae

tools/neutrons/export.xml

+14 −14
Original line number Diff line number Diff line 
<?xml version="1.0"?>

<tool name="Export Datasets" id="neutrons_export" version="0.2.0" profile="22.05">

<tool name="Export Datasets" id="neutrons_export" version="0.3.0" profile="22.05">

  <description>to SNS/HFIR storage</description>

    <requirements>

        <container type="docker">alpine:3.17</container>

    </requirements>

    <command><![CDATA[

        #from pathlib import Path

        #if $input_mode.input_mode_collection == 'true':

            mkdir -p $input_mode.export_folder &&

            #for $el in $input_mode.input:

        #for $s in $series

          #if $s.input_mode.input_mode_collection == 'true':

            mkdir -p $s.input_mode.export_folder &&

            #for $el in $s.input_mode.input:

               #set $name = str($el.element_identifier)

               #if Path($name).suffix == '':

                #set $name=$name + '.'+$el.ext

               #end if

               cp '$el' '$input_mode.export_folder/$name' &&

               echo '$input_mode.export_folder/$name' >> $output &&

               cp '$el' '$s.input_mode.export_folder/$name' &&

               echo '$s.input_mode.export_folder/$name' >> $output &&

            #end for

          #else:

            #for $i, $s in enumerate($input_mode.series)

                cp '${s.input}' '${s.export_path}' &&

                echo '${s.export_path}'>> $output &&

            #end for

                cp '${s.input_mode.input}' '${s.input_mode.export_path}' &&

                echo '${s.input_mode.export_path}'>> $output &&

          #end if

        #end for

        :

    ]]>

    </command>

  <inputs>

      <repeat name="series" title="Data">

       <conditional name="input_mode">

            <param name="input_mode_collection" type="boolean" truevalue="true" falsevalue="false" label="Export dataset collection"

            help=""/>
@@ -34,12 +35,11 @@ 
                <param name="export_folder" type="text" optional="false" default="" label="Export folder"/>

            </when>

            <when value="false">

                 <repeat name="series" title="Datasets">

                    <param name="input" type="data" label="Dataset"/>

                    <param name="export_path" type="text" optional="false" default="" label="Export path"/>

                </repeat>

            </when>

        </conditional>

       </repeat>

  </inputs>

    <outputs>

        <data name="output" auto_format="true" label="exported files"/>