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comparison ashlar.xml @ 1:f183d9de4622 draft

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planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 95998c84e130c9f3d2183591957464df7d90dd53
author goeckslab
date Wed, 24 Aug 2022 19:19:40 +0000
parents b3054f3d42b2
children 33ab2058c6d9
comparison
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0:b3054f3d42b2 1:f183d9de4622
1 <tool id="ashlar" name="ASHLAR" version="@VERSION@.6" profile="17.09"> 1 <tool id="ashlar" name="ASHLAR" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="19.01">
2 <description>Alignment by Simultaneous Harmonization of Layer/Adjacency Registration</description> 2 <description>Alignment by Simultaneous Harmonization of Layer/Adjacency Registration</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 6
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 @VERSION_CMD@ 8 <expand macro="version_cmd"/>
9 9
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 11
12 #def clean(file,type) 12 #def clean(file,type)
13 #set name_clean = str($file.element_identifier).replace('.ome.tiff','').replace('.tiff','').replace('.tiff.','') 13 #set name_clean = str($file.element_identifier).replace('.ome.tiff','').replace('.tiff','').replace('.tiff.','')
14 14
15 #if $type == "raw" 15 #if $type == "raw"
16 #set file_clean = $name_clean + ".ome.tiff" 16 #set file_clean = $name_clean + '.ome.tiff'
17 #elif $type == "ffp" 17 #elif $type == "ffp"
18 #set file_clean = $name_clean + "_ffp.ome.tiff" 18 #set file_clean = $name_clean + '_ffp.ome.tiff'
19 #elif $type == "dfp" 19 #elif $type == "dfp"
20 #set file_clean = $name_clean + "_dfp.ome.tiff" 20 #set file_clean = $name_clean + '_dfp.ome.tiff'
21 #end if 21 #end if
22 22
23 #return $file_clean 23 #return $file_clean
24 #end def 24 #end def
25 25
26 ## Link the illumination files to appropriate file extension 26 ## Link the illumination files to appropriate file extension
27 #for $dfp in $ldfp: 27 #if $ldfp
28 ln -s "$dfp" "$clean($dfp,"dfp")" && 28 #for $dfp in $ldfp:
29 #end for 29 ln -s '$dfp' '$clean($dfp,"dfp")' &&
30 #for $ffp in $lffp: 30 #end for
31 ln -s "$ffp" "$clean($ffp,"ffp")" && 31 #end if
32 #end for 32
33 #if $lffp
34 #for $ffp in $lffp:
35 ln -s '$ffp' '$clean($ffp,"ffp")' &&
36 #end for
37 #end if
33 38
34 @CMD_BEGIN@ 39 @CMD_BEGIN@
35 40
36 ## Supply the raw images 41 ## Supply the raw images
37 #for $raw in $lraw: 42 #for $raw in $lraw:
38 "$raw" 43 '$raw'
39 #end for 44 #end for
40 45
41 ## Additional arguments 46 ## Additional arguments
42 -m $max_shift 47 -m $max_shift
43 48
44 #if $flip_x 49 $flip_x
45 --flip-x 50 $flip_y
46 #end if
47
48 #if $flip_y
49 --flip-y
50 #end if
51 51
52 -c $adv.align_channel 52 -c $adv.align_channel
53 53
54 #if $adv.filter_sigma 54 #if $adv.filter_sigma
55 --filter-sigma $adv.filter_sigma 55 --filter-sigma $adv.filter_sigma
57 57
58 #if $adv.tile_size 58 #if $adv.tile_size
59 --tile-size $adv.tile_size 59 --tile-size $adv.tile_size
60 #end if 60 #end if
61 61
62 #if $lffp
62 --ffp 63 --ffp
63 #for $ffp in $lffp: 64 #for $ffp in $lffp:
64 "$clean($ffp,"ffp")" 65 '$clean($ffp,"ffp")'
65 #end for 66 #end for
67 #end if
68
69 #if $ldfp
66 --dfp 70 --dfp
67 #for $dfp in $ldfp: 71 #for $dfp in $ldfp:
68 "$clean($dfp,"dfp")" 72 '$clean($dfp,"dfp")'
69 #end for 73 #end for
70 --pyramid 74 #end if
75
76 $adv.pyramid
77 $adv.flip_mosaic_x
78 $adv.flip_mosaic_y
79
71 -f registered.ome.tif; 80 -f registered.ome.tif;
72 81
73 #if $upgrade.decide == "do_upgrade" 82 #if $upgrade.decide == "do_upgrade"
74 python ${__tool_directory__}/pyramid_upgrade.py 83 python3 '${__tool_directory__}/pyramid_upgrade.py'
75 registered.ome.tif 84 registered.ome.tif
76 85
77 #if $upgrade.markers_file 86 #if $upgrade.markers_file
78 -n `python "$get_markers" "${upgrade.markers_file}"` 87 -n `echo \$(cat $upgrade.markers_file | tail -n +2 | awk -F, '{print \$3}')`;
79 #end if 88 #end if
80 #end if 89 #end if
81 ]]></command> 90 ]]></command>
82 91
83 <configfiles>
84 <configfile name="get_markers">
85 import pandas as pd
86 import sys
87
88 marker_file = sys.argv[1]
89 df = pd.read_csv(marker_file)
90 print(' '.join(df['marker_name'].array))
91 </configfile>
92 </configfiles>
93
94
95
96 <inputs> 92 <inputs>
97 <param name="lraw" type="data_collection" format="tiff" collection_type="list" label="Raw Images"/> 93 <param name="lraw" type="data_collection" format="ome.tiff,tiff" collection_type="list" label="Raw Images"/>
98 <param name="ldfp" type="data_collection" format="tiff" collection_type="list" label="Deep Field Profile Images"/> 94 <param name="ldfp" type="data_collection" format="ome.tiff,tiff" collection_type="list" optional="true" label="Deep Field Profile Images"/>
99 <param name="lffp" type="data_collection" format="tiff" collection_type="list" label="Flat Field Profile Images"/> 95 <param name="lffp" type="data_collection" format="ome.tiff,tiff" collection_type="list" optional="true" label="Flat Field Profile Images"/>
100 96 <param name="flip_x" type="boolean" truevalue="--flip-x" falsevalue="" label="Flip X-axis"/>
101 <param name="flip_x" type="boolean" value="false" label="Flip X-axis"/> 97 <param name="flip_y" type="boolean" truevalue="--flip-y" falsevalue="" label="Flip Y-axis"/>
102 <param name="flip_y" type="boolean" value="false" label="Flip Y-axis"/>
103
104 <param name="max_shift" type="integer" value="30" label="Maximum allowed per-tile corrective shift" help="In micros"/> 98 <param name="max_shift" type="integer" value="30" label="Maximum allowed per-tile corrective shift" help="In micros"/>
105
106 <conditional name="upgrade"> 99 <conditional name="upgrade">
107 <param name="decide" type="select" label="Upgrade to BF6-Compliant OME-TIFF Pyramid"> 100 <param name="decide" type="select" label="Upgrade to BF6-Compliant OME-TIFF Pyramid">
108 <option value="do_upgrade">Upgrade Pyramid</option> 101 <option value="do_upgrade">Upgrade Pyramid</option>
109 <option value="dont_upgrade">Leave Legacy Pyramid</option> 102 <option value="dont_upgrade">Leave Legacy Pyramid</option>
110 </param> 103 </param>
116 </conditional> 109 </conditional>
117 <section name="adv" title="Advanced Options" expanded="false"> 110 <section name="adv" title="Advanced Options" expanded="false">
118 <param name="align_channel" type="integer" value="0" label="Align Channel Number"/> 111 <param name="align_channel" type="integer" value="0" label="Align Channel Number"/>
119 <param name="filter_sigma" type="float" optional="true" label="Sigma"/> 112 <param name="filter_sigma" type="float" optional="true" label="Sigma"/>
120 <param name="tile_size" type="integer" optional="true" label="Cyto Mask Channel"/> 113 <param name="tile_size" type="integer" optional="true" label="Cyto Mask Channel"/>
114 <param name="flip_mosaic_x" type="boolean" truevalue="--flip-mosaic-x" falsevalue="" label="Flip output image horizontally"/>
115 <param name="flip_mosaic_y" type="boolean" truevalue="--flip-mosaic-y" falsevalue="" label="Flip output image vertically"/>
116 <param name="pyramid" type="boolean" checked="true" truevalue="--pyramid" falsevalue="" label="Write output as a single pyramidal TIFF"/>
121 </section> 117 </section>
122 </inputs> 118 </inputs>
123 119
124 <outputs> 120 <outputs>
125 <data format="tiff" name="output" from_work_dir="registered.ome.tif" label="${tool.name} on ${on_string}"/> 121 <data format="ome.tiff" name="output" from_work_dir="registered.ome.tif" label="${tool.name} on ${on_string}"/>
126 </outputs> 122 </outputs>
123 <tests>
124 <test>
125 <param name="lraw">
126 <collection type="list">
127 <element name="rR1" value="ashlar_test_c0.tiff" />
128 <element name="rR2" value="ashlar_test_c1.tiff" />
129 </collection>
130 </param>
131 <output name="output" ftype="ome.tiff">
132 <assert_contents>
133 <has_size value="4000000" delta="1000000" />
134 </assert_contents>
135 </output>
136 </test>
137 </tests>
127 <help><![CDATA[ 138 <help><![CDATA[
128 Ashlar python package for microscopy registration, developed by HMS (repo: https://github.com/labsyspharm/ashlar) 139 --------------------------------------------------------------------------------
129 ashlar [-h] [-o DIR] [-c [CHANNEL]] 140 ASHLAR: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration
130 [--output-channels [CHANNEL [CHANNEL ...]]] [-m SHIFT] 141 --------------------------------------------------------------------------------
131 [--filter-sigma SIGMA] [-f FORMAT] [--pyramid]
132 [--tile-size PIXELS] [--ffp [FILE [FILE ...]]]
133 [--dfp [FILE [FILE ...]]] [--plates] [-q] [--version]
134 [FILE [FILE ...]]
135 142
136 Stitch and align one or more multi-series images 143 **Whole-slide microscopy image stitching and registration in Python**
137 144
138 positional arguments: 145 **Ashlar** performs fast, high-quality stitching of microscopy images. It also
139 FILE an image file to be processed (one file per cycle) 146 co-registers multiple rounds of cyclic imaging for methods such as CyCIF and
147 CODEX. Ashlar can read image data directly from BioFormats-supported microscope
148 vendor file formats as well as a directory of plain TIFF files. Output is saved
149 as pyramidal, tiled OME-TIFF.
140 150
141 optional arguments: 151 Note that Ashlar requires unstitched individual "tile" images as input, so it is
142 -h, --help show this help message and exit 152 not suitable for microscopes or slide scanners that only provide pre-stitched
143 -o DIR, --output DIR write output image files to DIR; default is the 153 images.
144 current directory
145 -c [CHANNEL], --align-channel [CHANNEL]
146 align images using channel number CHANNEL; numbering
147 starts at 0
148 --output-channels [CHANNEL [CHANNEL ...]]
149 output only channels listed in CHANNELS; numbering
150 starts at 0
151 -m SHIFT, --maximum-shift SHIFT
152 maximum allowed per-tile corrective shift in microns
153 --filter-sigma SIGMA width in pixels of Gaussian filter to apply to images
154 before alignment; default is 0 which disables
155 filtering
156 -f FORMAT, --filename-format FORMAT
157 use FORMAT to generate output filenames, with {cycle}
158 and {channel} as required placeholders for the cycle
159 and channel numbers; default is
160 cycle_{cycle}_channel_{channel}.tif
161 --pyramid write output as a single pyramidal TIFF
162 --tile-size PIXELS set tile width and height to PIXELS (pyramid output
163 only); default is 1024
164 --ffp [FILE [FILE ...]]
165 read flat field profile image from FILES; if specified
166 must be one common file for all cycles or one file for
167 each cycle
168 --dfp [FILE [FILE ...]]
169 read dark field profile image from FILES; if specified
170 must be one common file for all cycles or one file for
171 each cycle
172 --plates enable plate mode for HTS data
173 -q, --quiet suppress progress display
174 --version print version
175 154
176 OHSU Wrapper Repo: https://github.com/ohsu-comp-bio/ashlar 155 *Visit https://labsyspharm.github.io/ashlar/ for the most up-to-date information on ASHLAR.*
177 Conda Package Available From: https://anaconda.org/ohsu-comp-bio/ashlar
178 ]]></help> 156 ]]></help>
179 <expand macro="citations" /> 157 <expand macro="citations" />
180 </tool> 158 </tool>