# HG changeset patch
# User bgruening
# Date 1701886457 0
# Node ID 3085096f2b99351278c745be54f59e19e75d2c85

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 04eb6bf2ffe44b87f8c12134ac3bee33656f0673

diff -r 000000000000 -r 3085096f2b99 biaftplink.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/biaftplink.xml	Wed Dec 06 18:14:17 2023 +0000
@@ -0,0 +1,59 @@
+<tool id="bia_download" name="FTP Link for Bioimage Archive" version="@VERSION@+galaxy0" profile="22.05">
+    <description>Download images from Bioimage Archive</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="aggressive">
+<![CDATA[
+        wget -r 'ftp://ftp.ebi.ac.uk/biostudies/$mode/$path'/Files; 
+        #if '$ftp_output'
+            #set study = $path.split('/')[-1].rstrip('/')
+            curl https://www.ebi.ac.uk/biostudies/api/v1/studies/$study/info -s |jq -r .ftpLink >>ftpLink.txt
+        #end if
+]]>
+    </command>
+    <inputs>
+    <param name="mode" type="text" label="Storage mode" help="The storage mode, can be either nfs or fire."/>
+    <param name="path" type="text" label="The path of accession. e.g. S-BIAD/570/S-BIAD570 "/>
+        <param name="ftplink_output" type="boolean" label="Generate FTP links?" help="If set, a file containing FTP links associated with the accession will be generated." />
+    </inputs>
+    <outputs>
+        <data name="images" format="tiff">
+            <discover_datasets pattern="__name_and_ext__" format="tif,tiff" directory="ftp.ebi.ac.uk" visible="true" recurse="true" />
+        </data>
+        <data format="txt" name="ftplinks" from_work_dir="ftpLink.txt" label="FTP Links">
+            <filter>ftplink_output</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs='1'>
+            <param name="mode" value="fire" />
+            <param name="path" value="S-BIAD/961/S-BIAD961" />
+            <param name="ftplink_output" value="False" />
+            <output name="images">
+                <discovered_dataset designation="Study_Component-4_mznanog_mCherry-AAT" ftype="tif">
+                    <assert_contents><has_size value="14092624" /></assert_contents>
+                </discovered_dataset>
+            </output>
+        </test>
+        <test expect_num_outputs='2'>
+            <param name="mode" value="fire" />
+            <param name="path" value="S-BIAD/961/S-BIAD961" />
+            <param name="ftplink_output" value="True" />
+            <output name="images">
+                 <discovered_dataset designation="Study_Component-4_mznanog_mCherry-AAT" ftype="tif">
+                     <assert_contents><has_size value="14092624" /></assert_contents>
+                </discovered_dataset>
+            </output>
+               <output name="ftplinks" ftype="txt" file="ftpLink.txt" lines_diff="0" />
+            </test>
+    </tests>
+    <help>
+<![CDATA[
+        **What it does**
+        This tool downloads images from the Bioimage Archive and optionally outputs FTP links associated with the input accession.
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>
diff -r 000000000000 -r 3085096f2b99 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed Dec 06 18:14:17 2023 +0000
@@ -0,0 +1,21 @@
+<macros>
+    <token name="@VERSION@">0.1.0</token>
+    <xml name="requirements">
+        <requirements>
+	    <requirement type="package" version="1.20.3">wget</requirement>
+	    <requirement type="package" version="8.4.0">curl</requirement>
+	    <requirement type="package" version="1.6">jq</requirement>
+            <yield />
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+                @misc{bia,,
+                 title = "BioImage Archive Downloading via ftp",                 
+                 note = "https://www.ebi.ac.uk/bioimage-archive/help-download/",
+                 url = "https://www.ebi.ac.uk/bioimage-archive/help-download/"}</citation>
+        </citations>
+    </xml>
+</macros>
+
diff -r 000000000000 -r 3085096f2b99 test-data/ftpLink.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ftpLink.txt	Wed Dec 06 18:14:17 2023 +0000
@@ -0,0 +1,1 @@
+ftp://ftp.ebi.ac.uk/biostudies/fire/S-BIAD/961/S-BIAD961