Commit 79b69c86 authored by Yakubov, Sergey's avatar Yakubov, Sergey
Browse files

Merge branch '107-make-recursive-folder-ingress-optional' into 'dev' 

add option for recursion to ingress folder tool

Closes #107

See merge request ndip/galaxy-tools!183
parents efa31167 7c7b87a3

tools/neutrons/ingress_folder.xml

+5 −4
Original line number Diff line number Diff line 
<?xml version="1.0"?>

<tool name="Register Data Folder" id="neutrons_ingress_folder" version="0.1.0" profile="22.05">

<tool name="Register Data Folder" id="neutrons_ingress_folder" version="0.1.1" profile="22.05">

    <description>in Galaxy </description>

    <requirements>

        <container type="docker">python:3.10-bullseye</container>
@@ -10,7 +10,7 @@ 
        exit 1;

      fi &&

      mkdir output &&

      python -c "import glob; [print(f) for f in glob.glob('$folder/' + ('$filter' or '**'), recursive=True)]" |

      python -c "import glob; [print(f) for f in glob.glob('$folder/' + ('$filter' or '**'), recursive=$recursive)]" |

      while IFS= read -r file; do

        if [ -f \$file ]; then

         relative_path="\${file#$folder}" &&
@@ -25,14 +25,15 @@ 
      done

    ]]></command>

    <inputs>

        <param name="folder" type="text" label="Folder to Ingress" value="" optional="false"/>

        <param name="folder" type="text" label="Folder to ingress" value="" optional="false"/>

        <param name="recursive" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Recursive ingress"/>

        <param name="filter" type="text" label="Filter Files" value="" optional="true" help="Wildcard to filter ingressed data.

        E.g. *.dat (all .dat files in the folder, no recursion); subfolder/*.dat (.dat files in subfolder);

        **/*.dat - all .dat files in the folder and subfolders;

        empty string (or **) - all files in the folder and all subfolders.

        "/>

        <param name="collection_name" type="text" label="New collection name" value="" optional="true"/>

        <param name="debug_output" type="boolean" truevalue="true" falsevalue="false" default="false" label="Output log file"

        <param name="debug_output" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output log file"

            help=""/>



    </inputs>