--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/idr_download_by_ids.xml	Sat Feb 08 13:24:39 2020 -0500
@@ -0,0 +1,257 @@
+<?xml version="1.0"?>
+<tool id="idr_download_by_ids" name="IDR Download" version="0.9" profile="18.09">
+    <description>- download images from the Image Data Resource using image IDs</description>
+    <macros>
+        <xml name="region_spec" token_pos="upper-left corner">
+            <param name="x_coord" type="integer" value="0" min="0"
+            label="x-coordinate of region @POS@" />
+            <param name="y_coord" type="integer" value="0" min="0"
+            label="y-coordinate of region @POS@" />
+            <param name="width" type="integer" value="0" min="0"
+            label="Region width"
+            help="Set to zero to extend the rectangle maximally along the x-axis of the image" />
+            <param name="height" type="integer" value="0" min="0"
+            label="Region height"
+            help="Set to zero to extend the rectangle maximally along the y-axis of the image" />
+        </xml>
+    </macros>
+    <requirements>
+        <requirement type="package" version="5.6.0">python-omero</requirement>
+        <requirement type="package" version="3.1.3">matplotlib</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        mkdir downloads && cd downloads &&
+        #if str($image_ids.source) == 'link':
+            python -c 'print("${image_ids.id_spec}".replace(",", "|").split("?show=")[-1].replace("|", "\n"))'
+            ## https://idr.openmicroscopy.org/webclient/?show=image-3426274|image-3426275|image-3426276|image-3426277
+        #else:
+            cat '${image_ids.id_spec}'
+        #end if
+        | python '$__tool_directory__/idr_download_by_ids.py' 
+        #set $channel = str($channel).strip()
+        #if $channel:
+            -c '$channel'
+        #end if
+        -f $frame
+        -z $z_section
+        #if str($clip_image.select):
+            ${clip_image.select} ${clip_image.x_coord} ${clip_image.y_coord} ${clip_image.width} ${clip_image.height}
+        #end if
+        $skip_failed
+
+        2> >(tee -a $out_log >&2)
+    ]]></command>
+<inputs>
+        <conditional name="image_ids">
+            <param name="source" type="select" label="How would you like to specify the IDs of images to download?">
+                <option value="link">As text (comma-separated list of IDs or a valid IDR link)</option>
+                <option value="dataset">As a dataset (one image ID per line)</option>
+            </param>
+            <when value="link">
+                <param name="id_spec" type="text"
+                label="Image IDs to download"
+                help="You can enter a single image-id, or a comma (or '|')-separated list of IDs. Alternatively, you can paste here a link to an image selection obtained through the IDR webclient.">
+                    <sanitizer>
+                        <valid><add value="|" /></valid>
+                    </sanitizer>
+                </param>
+            </when>
+            <when value="dataset">
+                <param name="id_spec" type="data" format="txt"
+                label="Select a dataset with image IDs (one per line)" />
+            </when>
+        </conditional>
+        <param name="channel" type="text"
+        label="Name of the channel to download"
+        help="For all image IDs only the specified channel will be downloaded. If left empty, the first channel (whatever this is) will be downloaded by default." />
+        <param name="z_section" type="integer" value="0" min="0"
+        label="z-plane of images to download" />
+        <param name="frame" type="integer" value="0" min="0"
+        label="Image frame to download" />
+        <conditional name="clip_image">
+            <param name="select" type="select"
+            label="Limit the download to a selected region of the image?">
+                <option value="">No, download the entire image plane</option>
+                <option value="--rectangle">Specify a region using its upper-left corner</option>
+                <option value="--center">Specify a width x height region around a central point</option>
+            </param>
+            <when value="" />
+            <when value="--rectangle">
+                <expand macro="region_spec" />
+            </when>
+            <when value="--center">
+                <expand macro="region_spec" pos="center" />
+            </when>
+        </conditional>
+        <param name="skip_failed" type="boolean" checked="false" truevalue="--skip-failed" falsevalue=""
+        label="Skip failed retrievals?"
+        help="By default the tool will fail with an error on the first non-retrievable image ID. Here, you can choose to skip non-retrievable image IDs and continue downloading the available ones instead. The error log will contain warnings about failed IDs in this case." />
+    </inputs>
+    <outputs>
+        <data name="out_log" format="txt" label="${tool.name} error log" />
+        <collection name="output_file" type="list">
+            <discover_datasets pattern="__name_and_ext__" directory="downloads" />
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="source" value="dataset" />
+            <param name="id_spec" value="ids.txt" />
+            <param name="channel" value="615.0" />
+            <conditional name="clip_image">
+                <param name="select" value="--rectangle" />
+                <param name="x_coord" value="3" />
+                <param name="y_coord" value="3" />
+                <param name="width" value="5" />
+                <param name="height" value="5" />
+            </conditional>
+            <param name="frame" value="2" />
+            <output_collection name="output_file" type="list">
+                <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ_1884807_3_3_5_5" file="test1.tiff"/>
+            </output_collection>
+        </test>
+        <test>
+            <param name="source" value="link" />
+            <param name="id_spec" value="1884807" />
+            <param name="channel" value="615.0" />
+            <conditional name="clip_image">
+                <param name="select" value="--rectangle" />
+                <param name="x_coord" value="3" />
+                <param name="y_coord" value="3" />
+                <param name="width" value="5" />
+                <param name="height" value="5" />
+            </conditional>
+            <param name="frame" value="2" />
+            <output_collection name="output_file" type="list">
+                <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ_1884807_3_3_5_5" file="test1.tiff"/>
+            </output_collection>
+        </test>
+        <test>
+            <param name="source" value="link" />
+            <param name="id_spec" value="1884807" />
+            <param name="channel" value="615.0" />
+            <conditional name="clip_image">
+                <param name="select" value="--center" />
+                <param name="x_coord" value="5" />
+                <param name="y_coord" value="5" />
+                <param name="width" value="5" />
+                <param name="height" value="5" />
+            </conditional>
+            <param name="frame" value="2" />
+            <output_collection name="output_file" type="list">
+                <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ_1884807_3_3_5_5" file="test1.tiff"/>
+            </output_collection>
+        </test>
+        <test>
+            <param name="source" value="link" />
+            <param name="id_spec" value="https://idr.openmicroscopy.org/webclient/?show=image-9036708|image-9036710|image-9036711" />
+            <param name="channel" value="Spo20(51-91)" />
+            <param name="z_section" value="4" />
+            <conditional name="clip_image">
+                <param name="select" value="" />
+            </conditional>
+            <param name="frame" value="20" />
+            <output_collection name="output_file" type="list" count="3">
+                <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D_9036711_0_0_1024_1024">
+                    <assert_contents>
+                        <has_size value="4194510" />
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <output name="out_log">
+                <assert_contents>
+                    <has_text text="(ID: 9036710): Specified image plane (4) is out of bounds"/>
+                    <has_n_lines n="1"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_failure="true">
+            <!-- Test behavior with non-existing image-ID 9036708999 -->
+            <param name="source" value="link" />
+            <param name="id_spec" value="https://idr.openmicroscopy.org/webclient/?show=image-9036708999|image-9036710|image-9036711" />
+            <param name="channel" value="Spo20(51-91)" />
+            <param name="z_section" value="4" />
+            <conditional name="clip_image">
+                <param name="select" value="" />
+            </conditional>
+            <param name="frame" value="20" />
+        </test>
+        <test>
+            <!-- Repeat test with non-existing image-ID 9036708999,
+            but use skip-failed option -->
+            <param name="source" value="link" />
+            <param name="id_spec" value="https://idr.openmicroscopy.org/webclient/?show=image-9036708999|image-9036710|image-9036711" />
+            <param name="channel" value="Spo20(51-91)" />
+            <param name="z_section" value="4" />
+            <conditional name="clip_image">
+                <param name="select" value="" />
+            </conditional>
+            <param name="frame" value="20" />
+            <param name="skip_failed" value="true" />
+            <output_collection name="output_file" type="list" count="2">
+                <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D_9036711_0_0_1024_1024">
+                    <assert_contents>
+                        <has_size value="4194510" />
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <output name="out_log">
+                <assert_contents>
+                    <has_text text="9036708999: Unable to find an image with this ID in the database. Skipping download!" />
+                    <has_text text="(ID: 9036710): Specified image plane (4) is out of bounds" />
+                    <has_n_lines n="2"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+Download image data from the IDR_ (Image Data Resource) - a public repository
+of reference image datasets from published scientific studies.
+
+.. _IDR: https://idr.openmicroscopy.org/about/
+
+-----
+
+.. class:: infomark
+
+**Input**
+
+A set of image IDs as can be obtained from the IDR webclient_ like this:
+
+1. select the images you want to download
+2. click on the 'Link' button on the top right of the page and copy the provided
+   URL
+3. paste the URL into the input field of this tool, for example: ::
+
+    https://idr.openmicroscopy.org/webclient/?show=image-9036708|image-9036710|image-9036711
+
+Alternatively, you can simply provide a list of known image IDs in the text
+input field (comma or '|'-separated ), or as an input file (each ID on a
+separate line).
+
+Most images in the IDR have more than two dimensions. Thus, there are
+parameters available which allow you to select a particular recording channel,
+z-plane or time frame to download.
+You can also select a region which will be used to crop the images, rather
+than downloading the entire file.
+
+.. _webclient: https://idr.openmicroscopy.org/
+
+
+-----
+
+.. class:: infomark
+
+**Output**
+
+Downloaded images will be saved in TIFF format. If you selected multiple image
+IDs to download, these will be saved as elements of a collection.
+
+The accompanying error log dataset may hold valuable information about requests
+that could not be fulfilled exactly as specified, or that were found to be
+ambiguous.
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1038/nmeth.4326</citation>
+    </citations>
+</tool>