Add BioStudies upload tool

tools/biostudies_upload/biostudies_upload.xml

@@ -0,0 +1,88 @@
+<tool id="biostudies_upload" name="BioStudies upload" version="0.1" profile="25.1">
+    <description>Upload data to BioStudies using Aspera high-speed transfer</description>
+    <xrefs>
+        <xref type="bio.tools">aspera</xref>
+    </xrefs>
+    <requirements>
+        <requirement type="package" version="4.20.0">aspera-cli</requirement>
+        <credentials name="biostudies" version="0.1" label="BioStudies" description="The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database can accept a wide range of types of studies described via a simple format. It also enables manuscript authors to submit supplementary information and link to it from the publication.">
+            <secret name="password" inject_as_env="BIOSTUDIES_PASS" optional="false" label="Password" description="Your password to upload to BioStudies"/>
+            <secret name="secret_dir" inject_as_env="BIOSTUDIES_SECRET_DIR" optional="false" label="Secret Directory" description="Secret directory root where your files will be uploaded"/>
+        </credentials>
+    </requirements>
+    <command><![CDATA[
+## Determine what to upload based on the dataset format
+## For regular files, we can upload directly
+#set $upload_path = $input_to_upload
+#if $input_to_upload.extension == 'zarr' and not $input_to_upload.is_deferred
+    ## For Zarr datasets, we need to upload the folder structure
+    ## Append the store_root to the extra_files_path to get the full path to the zarr store
+    ## TODO: verify if we need to use '$input_to_upload.extra_files_path/$input_to_upload.metadata.store_root'
+    ##       for zarr.zip datasets that uncompress into a subfolder pointed by store_root
+    #set $upload_path = $input_to_upload.extra_files_path
+#end if
+ascli config ascp install > /dev/null 2>&1 &&
+ascli server upload '$upload_path' --url=ssh://fasp.ebi.ac.uk:33001 --username=bs-upload --password=\$BIOSTUDIES_PASS --to-folder=\$BIOSTUDIES_SECRET_DIR/$target_dir 2>&1 | tee $stdout
+    ]]>
+    </command>
+    <inputs>
+        <param name="input_to_upload" type="data" format="data" label="Input file"/>
+        <param name="target_dir" type="text" optional="false" label="Target remote folder name"/>
+    </inputs>
+    <outputs>
+        <data name="stdout" format="txt" label="Upload Log"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_to_upload" value="smaller_MT_image.tiff"/>
+            <param name="target_dir" value="galaxy_tool_test"/>
+            <output name="stdout">
+                <assert_contents>
+                    <has_text text="100%"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+This tool uploads data files to the BioStudies database at EMBL-EBI using the Aspera high-speed file transfer protocol. BioStudies is a repository that holds descriptions of biological studies and associated data that may not fit in other structured archives.
+
+The tool uses Aspera CLI to securely transfer your files to a specified directory in your BioStudies submission area.
+
+------
+
+**Inputs**
+
+- **Input file**: Any biological study data file you wish to upload
+- **Target remote folder name**: Name of the destination folder in your BioStudies secret directory where files will be uploaded
+
+------
+
+**Outputs**
+
+- **Upload Log**: A text file containing the transfer process details.
+
+------
+
+**Authentication**
+
+This tool requires BioStudies credentials configured in Galaxy:
+
+- **Password**: Your BioStudies upload password
+- **Secret Directory**: The root directory path where you have permission to upload files in BioStudies
+
+------
+
+**Additional Information**
+
+The tool uses Aspera's FASP (Fast and Secure Protocol) technology for accelerated file transfer, which is particularly useful for large datasets.
+
+For more information about BioStudies, visit: https://www.ebi.ac.uk/biostudies/
+
+
+    ]]>    </help>
+    <citations>
+        <citation type="doi">10.1126/science.abl5197</citation>
+    </citations>
+</tool>