# HG changeset patch
# User galaxy-australia
# Date 1728276502 0
# Node ID 7f6de5d9fb50ba9fd33cf00b198d7edc0320562d

planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnetfilesender commit 192bb5e7bd10d911d7bd8c91ca9f3c88ae6da334

diff -r 000000000000 -r 7f6de5d9fb50 filesender.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filesender.xml	Mon Oct 07 04:48:22 2024 +0000
@@ -0,0 +1,79 @@
+<tool id="aarnet_filesender" name="AARNet FileSender" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>transfer files to AARNet's FileSender Service</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="exit_code"><![CDATA[
+#if $test != "":
+    filesender -h &&
+    exit 0;
+#end if
+
+#set $apiuser = $__user__.extra_preferences.get('aarnet_filesender_account|username', "").strip()
+#set $apikey = $__user__.extra_preferences.get('aarnet_filesender_account|apikey', "").strip()
+
+#if $apiuser == "" or $apikey == "":
+    echo "ERROR: Please enter your FileSender Username in your user preferences under the AARNet FileSender Account Info section" >&2 &&
+    exit 1;
+#end if
+
+#if $to == "":
+    echo "WARNING: recipent email not set, setting to $__user_email__" &&
+    #set $to = $__user_email__
+#end if
+
+mkdir filestosend &&
+
+#for $file in $data
+    if [ -f "filestosend/${file.element_identifier}" ]; then
+        echo "ERROR: two datasets have the same name (${file.element_identifier})" &&
+        exit 1;
+    fi &&
+    ln -s "$file" "filestosend/${file.element_identifier}" &&
+#end for
+
+filesender -p -u '$apiuser' -a '$apikey' -b https://filesender.aarnet.edu.au/rest.php -f "galaxy-no-reply@usegalaxy.org.au" -r '$to' filestosend >$output 2>&1
+    ]]></command>
+    <inputs>
+        <param name="data" type="data" format="txt,data" multiple="true" optional="false" label="Datasets to be sent:"/>
+        <param name="to" type="text" optional="true" label="Email address of recipent:">
+            <sanitizer sanitize="False"/>
+        </param>
+        <param name="test" type="hidden" value=""/>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" hidden="false"/>
+    </outputs>
+    <tests>
+        <test expect_exit_code="1" expect_failure="true">
+            <param name="data" value="summary_statistics.txt"/>
+            <assert_stderr>
+                <has_text text="ERROR: Please enter your FileSender Username in your user preferences under the AARNet FileSender Account Info section"/>
+            </assert_stderr>
+        </test>
+        <test>
+            <param name="data" value="summary_statistics.txt"/>
+            <param name="test" value="true"/>
+            <assert_stdout>
+                <has_text text="File Sender CLI client"/>
+            </assert_stdout>
+        </test>
+    </tests>
+    <help>
+**What it does**
+        Send dataset(s) from Galaxy to anyone via AARNet's FileSender service.
+
+**Remarks**
+        This tool leverages AARNet's FileSender (https://filesender.aarnet.edu.au)
+        to send files out of Galaxy.
+    </help>
+    <citations>
+        <citation type="bibtex">
+           @misc{FileSenderCLI_github,
+           title={FileSenderCLI Github page},
+           url = {https://github.com/madsi1m/FileSenderCLI},}
+        </citation>
+    </citations>
+</tool>
diff -r 000000000000 -r 7f6de5d9fb50 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Mon Oct 07 04:48:22 2024 +0000
@@ -0,0 +1,13 @@
+<macros>
+    <token name="@TOOL_VERSION@">v3.0.0</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">22.05</token>
+    <xml name="requirements">
+         <requirements>
+             <requirement type="package" version="@TOOL_VERSION@">filesendercli</requirement>
+         </requirements>
+    </xml>
+    <xml name="version_command">
+        <version_command>filesender --help | grep 'File Sender CLI client.'</version_command>
+    </xml>
+</macros>
diff -r 000000000000 -r 7f6de5d9fb50 test-data/output.log
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.log	Mon Oct 07 04:48:22 2024 +0000
@@ -0,0 +1,3 @@
+Uploading: Xnatutils on data 2424: log 100%
+Xnatutils on data 2424: log complete
+Upload Complete
diff -r 000000000000 -r 7f6de5d9fb50 test-data/summary_statistics.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summary_statistics.txt	Mon Oct 07 04:48:22 2024 +0000
@@ -0,0 +1,5 @@
+Core genes	(99% <= strains <= 100%)	251
+Soft core genes	(95% <= strains < 99%)	0
+Shell genes	(15% <= strains < 95%)	0
+Cloud genes	(0% <= strains < 15%)	0
+Total genes	(0% <= strains <= 100%)	251
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