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comparison ashlar.xml @ 3:ef68bc2a4dbc draft default tip

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planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 69f200fcfa0b1d17de50466c51d8c5468fdeb54c
author goeckslab
date Fri, 09 Feb 2024 22:48:46 +0000
parents 33ab2058c6d9
children
comparison
equal deleted inserted replaced
2:33ab2058c6d9 3:ef68bc2a4dbc
49 $flip_x 49 $flip_x
50 $flip_y 50 $flip_y
51 51
52 -c $adv.align_channel 52 -c $adv.align_channel
53 53
54 #if $adv.stitch_alpha
55 --stitch-alpha $adv.stitch_alpha
56 #end if
57
54 #if $adv.filter_sigma 58 #if $adv.filter_sigma
55 --filter-sigma $adv.filter_sigma 59 --filter-sigma $adv.filter_sigma
56 #end if 60 #end if
57 61
58 #if $adv.tile_size 62 #if $adv.tile_size
71 #for $dfp in $ldfp: 75 #for $dfp in $ldfp:
72 '$clean($dfp,"dfp")' 76 '$clean($dfp,"dfp")'
73 #end for 77 #end for
74 #end if 78 #end if
75 79
76 $adv.pyramid
77 $adv.flip_mosaic_x 80 $adv.flip_mosaic_x
78 $adv.flip_mosaic_y 81 $adv.flip_mosaic_y
79 82
80 -f registered.ome.tif; 83 -o registered.ome.tif;
81
82 #if $upgrade.decide == "do_upgrade"
83 python3 '${__tool_directory__}/pyramid_upgrade.py'
84 registered.ome.tif
85
86 #if $upgrade.markers_file
87 -n `echo \$(cat $upgrade.markers_file | tail -n +2 | awk -F, '{print \$3}')`;
88 #end if
89 #end if
90 ]]></command> 84 ]]></command>
91 85
92 <inputs> 86 <inputs>
93 <param name="lraw" type="data_collection" format="ome.tiff,tiff" collection_type="list" label="Raw Images"/> 87 <param name="lraw" type="data_collection" format="ome.tiff,tiff" collection_type="list" label="Raw Images"/>
94 <param name="ldfp" type="data_collection" format="ome.tiff,tiff" collection_type="list" optional="true" label="Deep Field Profile Images"/> 88 <param name="ldfp" type="data_collection" format="ome.tiff,tiff" collection_type="list" optional="true" label="Deep Field Profile Images"/>
95 <param name="lffp" type="data_collection" format="ome.tiff,tiff" collection_type="list" optional="true" label="Flat Field Profile Images"/> 89 <param name="lffp" type="data_collection" format="ome.tiff,tiff" collection_type="list" optional="true" label="Flat Field Profile Images"/>
96 <param name="flip_x" type="boolean" truevalue="--flip-x" falsevalue="" label="Flip X-axis"/> 90 <param name="flip_x" type="boolean" truevalue="--flip-x" falsevalue="" label="Flip X-axis"/>
97 <param name="flip_y" type="boolean" truevalue="--flip-y" falsevalue="" label="Flip Y-axis"/> 91 <param name="flip_y" type="boolean" truevalue="--flip-y" falsevalue="" label="Flip Y-axis"/>
98 <param name="max_shift" type="integer" value="30" label="Maximum allowed per-tile corrective shift" help="In micros"/> 92 <param name="max_shift" type="integer" value="30" label="Maximum allowed per-tile corrective shift" help="In micros"/>
99 <conditional name="upgrade">
100 <param name="decide" type="select" label="Upgrade to BF6-Compliant OME-TIFF Pyramid">
101 <option value="do_upgrade">Upgrade Pyramid</option>
102 <option value="dont_upgrade">Leave Legacy Pyramid</option>
103 </param>
104 <when value="do_upgrade">
105 <param name="markers_file" type="data" format="csv,tabular" optional="true" label="Markers File (optional)"/>
106 </when>
107 <when value="dont_upgrade">
108 </when>
109 </conditional>
110 <section name="adv" title="Advanced Options" expanded="false"> 93 <section name="adv" title="Advanced Options" expanded="false">
111 <param name="align_channel" type="integer" value="0" label="Align Channel Number"/> 94 <param name="align_channel" type="integer" value="0" label="Align Channel Number"/>
95 <param name="stitch_alpha" type="float" optional="true" label="Alpha"/>
112 <param name="filter_sigma" type="float" optional="true" label="Sigma"/> 96 <param name="filter_sigma" type="float" optional="true" label="Sigma"/>
113 <param name="tile_size" type="integer" optional="true" label="Cyto Mask Channel"/> 97 <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"/> 98 <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"/> 99 <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"/>
117 </section> 100 </section>
118 </inputs> 101 </inputs>
119 102
120 <outputs> 103 <outputs>
121 <data format="ome.tiff" name="output" from_work_dir="registered.ome.tif" label="${tool.name} on ${on_string}"/> 104 <data format="ome.tiff" name="output" from_work_dir="registered.ome.tif" label="${tool.name} on ${on_string}"/>
128 <element name="rR2" value="ashlar_test_c1.tiff" /> 111 <element name="rR2" value="ashlar_test_c1.tiff" />
129 </collection> 112 </collection>
130 </param> 113 </param>
131 <output name="output" ftype="ome.tiff"> 114 <output name="output" ftype="ome.tiff">
132 <assert_contents> 115 <assert_contents>
133 <has_size value="4000000" delta="1000000" /> 116 <has_size value="500000" delta="400000" />
134 </assert_contents> 117 </assert_contents>
135 </output> 118 </output>
136 </test> 119 </test>
137 </tests> 120 </tests>
138 <help><![CDATA[ 121 <help><![CDATA[