Mercurial > repos > galaxy-australia > aarnet_filesender
changeset 0:7f6de5d9fb50 draft
planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnetfilesender commit 192bb5e7bd10d911d7bd8c91ca9f3c88ae6da334
| author | galaxy-australia |
|---|---|
| date | Mon, 07 Oct 2024 04:48:22 +0000 |
| parents | |
| children | 17787c79af44 |
| files | filesender.xml macros.xml test-data/output.log test-data/summary_statistics.txt |
| diffstat | 4 files changed, 100 insertions(+), 0 deletions(-) [+] |
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--- /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>
--- /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>
--- /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
--- /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 \ No newline at end of file