Mercurial > repos > perssond > ashlar
changeset 4:0b8423c7ee3e draft default tip
planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit d1f9d43d20432cc958e340271ba63c85a17ff338
| author | goeckslab |
|---|---|
| date | Wed, 26 Feb 2025 18:09:34 +0000 |
| parents | ef68bc2a4dbc |
| children | |
| files | ashlar.xml macros.xml rename_channels.py test-data/ashlar_test_markers.csv |
| diffstat | 4 files changed, 125 insertions(+), 2 deletions(-) [+] |
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--- a/ashlar.xml Fri Feb 09 22:48:46 2024 +0000 +++ b/ashlar.xml Wed Feb 26 18:09:34 2025 +0000 @@ -1,4 +1,4 @@ -<tool id="ashlar" name="ASHLAR" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="19.01"> +<tool id="ashlar" name="ASHLAR" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01"> <description>Alignment by Simultaneous Harmonization of Layer/Adjacency Registration</description> <macros> <import>macros.xml</import> @@ -81,6 +81,12 @@ $adv.flip_mosaic_y -o registered.ome.tif; + + #if $rename.decide == "do_rename" + python3 '${__tool_directory__}/rename_channels.py' + --image registered.ome.tif + --markers '$rename.markers_file'; + #end if ]]></command> <inputs> @@ -90,6 +96,17 @@ <param name="flip_x" type="boolean" truevalue="--flip-x" falsevalue="" label="Flip X-axis"/> <param name="flip_y" type="boolean" truevalue="--flip-y" falsevalue="" label="Flip Y-axis"/> <param name="max_shift" type="integer" value="30" label="Maximum allowed per-tile corrective shift" help="In micros"/> + <conditional name="rename"> + <param name="decide" type="select" label="Rename channels in OME-XML metadata"> + <option value="do_rename">Rename channels</option> + <option value="dont_rename" selected="true">Leave channel indices</option> + </param> + <when value="do_rename"> + <param name="markers_file" type="data" format="csv" label="Markers File"/> + </when> + <when value="dont_rename"> + </when> + </conditional> <section name="adv" title="Advanced Options" expanded="false"> <param name="align_channel" type="integer" value="0" label="Align Channel Number"/> <param name="stitch_alpha" type="float" optional="true" label="Alpha"/> @@ -117,6 +134,28 @@ </assert_contents> </output> </test> + <test> + <param name="lraw"> + <collection type="list"> + <element name="rR1" value="ashlar_test_c0.tiff" /> + <element name="rR2" value="ashlar_test_c1.tiff" /> + </collection> + </param> + <conditional name="rename"> + <param name="decide" value="do_rename" /> + <param name="markers_file" value="ashlar_test_markers.csv" /> + </conditional> + <output name="output" ftype="ome.tiff"> + <assert_contents> + <has_size value="500000" delta="400000" /> + </assert_contents> + </output> + <assert_stdout> + <has_text text="DAPI" /> + <has_text text="CD3" /> + <has_text text="µm" /> + </assert_stdout> + </test> </tests> <help><![CDATA[ --------------------------------------------------------------------------------
--- a/macros.xml Fri Feb 09 22:48:46 2024 +0000 +++ b/macros.xml Wed Feb 26 18:09:34 2025 +0000 @@ -17,6 +17,6 @@ </xml> <token name="@TOOL_VERSION@">1.18.0</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@CMD_BEGIN@">ashlar</token> </macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rename_channels.py Wed Feb 26 18:09:34 2025 +0000 @@ -0,0 +1,81 @@ +# ------------------------------------------------------------------------------------ +# Stripped down and modified from: +# https://github.com/ohsu-comp-bio/ashlar/blob/master/pyramid_upgrade.py +# ------------------------------------------------------------------------------------ + +import argparse +import csv +import xml.etree.ElementTree + +from tifffile import tiffcomment + + +def fix_attrib_namespace(elt): + """Prefix un-namespaced XML attributes with the tag's namespace.""" + # This fixes ElementTree's inability to round-trip XML with a default + # namespace ("cannot use non-qualified names with default_namespace option" + # error). 7-year-old BPO issue here: https://bugs.python.org/issue17088 + # Code inspired by https://gist.github.com/provegard/1381912 . + if elt.tag[0] == "{": + uri, _ = elt.tag[1:].rsplit("}", 1) + new_attrib = {} + for name, value in elt.attrib.items(): + if name[0] != "{": + # For un-namespaced attributes, copy namespace from element. + name = f"{{{uri}}}{name}" + new_attrib[name] = value + elt.attrib = new_attrib + for child in elt: + fix_attrib_namespace(child) + + +def main(image_fh, marker_file): + """ + Parameters + --------- + image_fh : str + File path to the OME Tiff image. + marker_file : str + File path to CSV containing marker name information. + """ + + # parse marker file, create list of new marker names + new_channel_names = [] + with open(marker_file, newline='') as csvfile: + reader = csv.DictReader(csvfile) + for row in reader: + new_channel_names.append(row['marker_name']) + + # read OME-XML metadata and parse down to channels + xml_ns = {"ome": "http://www.openmicroscopy.org/Schemas/OME/2016-06"} + root = xml.etree.ElementTree.fromstring(tiffcomment(image_fh)) + image = root.find("ome:Image", xml_ns) + pixels = image.find("ome:Pixels", xml_ns) + channels = pixels.findall("ome:Channel", xml_ns) + + # name channels + for channel, name in zip(channels, new_channel_names): + channel.attrib["Name"] = name + + # encode new xml and set image metadata + fix_attrib_namespace(root) + new_ome_xml = xml.etree.ElementTree.tostring( + root, + encoding='utf-8', + xml_declaration=True, + default_namespace=xml_ns["ome"]) + + tiffcomment(image_fh, comment=new_ome_xml) + + print("Updated OME-TIFF metadata:") + print(tiffcomment(image_fh)) + + +if __name__ == '__main__': + aparser = argparse.ArgumentParser() + aparser.add_argument("-i", "--image", dest="image", required=True) + aparser.add_argument("-m", "--markers", dest="markers", required=True) + + args = aparser.parse_args() + + main(args.image, args.markers)