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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
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4
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1 <tool id="ashlar" name="ASHLAR" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
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2 <description>Alignment by Simultaneous Harmonization of Layer/Adjacency Registration</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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7 <expand macro="requirements"/>
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8 <expand macro="version_cmd"/>
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9
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10 <command detect_errors="aggressive"><![CDATA[
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12 #def clean(file,type)
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13 #set name_clean = str($file.element_identifier).replace('.ome.tiff','').replace('.tiff','').replace('.tiff.','')
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15 #if $type == "raw"
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16 #set file_clean = $name_clean + '.ome.tiff'
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17 #elif $type == "ffp"
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18 #set file_clean = $name_clean + '_ffp.ome.tiff'
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19 #elif $type == "dfp"
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20 #set file_clean = $name_clean + '_dfp.ome.tiff'
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21 #end if
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23 #return $file_clean
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24 #end def
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26 ## Link the illumination files to appropriate file extension
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27 #if $ldfp
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28 #for $dfp in $ldfp:
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29 ln -s '$dfp' '$clean($dfp,"dfp")' &&
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30 #end for
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31 #end if
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33 #if $lffp
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34 #for $ffp in $lffp:
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35 ln -s '$ffp' '$clean($ffp,"ffp")' &&
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36 #end for
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37 #end if
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39 @CMD_BEGIN@
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41 ## Supply the raw images
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42 #for $raw in $lraw:
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43 '$raw'
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44 #end for
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46 ## Additional arguments
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47 -m $max_shift
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48
1
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49 $flip_x
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50 $flip_y
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51
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52 -c $adv.align_channel
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53
3
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54 #if $adv.stitch_alpha
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55 --stitch-alpha $adv.stitch_alpha
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56 #end if
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57
0
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58 #if $adv.filter_sigma
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59 --filter-sigma $adv.filter_sigma
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60 #end if
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61
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62 #if $adv.tile_size
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63 --tile-size $adv.tile_size
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64 #end if
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65
1
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66 #if $lffp
0
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67 --ffp
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68 #for $ffp in $lffp:
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69 '$clean($ffp,"ffp")'
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70 #end for
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71 #end if
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73 #if $ldfp
0
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74 --dfp
1
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75 #for $dfp in $ldfp:
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76 '$clean($dfp,"dfp")'
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77 #end for
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78 #end if
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80 $adv.flip_mosaic_x
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81 $adv.flip_mosaic_y
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82
3
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83 -o registered.ome.tif;
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84
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85 #if $rename.decide == "do_rename"
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86 python3 '${__tool_directory__}/rename_channels.py'
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87 --image registered.ome.tif
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88 --markers '$rename.markers_file';
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89 #end if
0
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90 ]]></command>
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91
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92 <inputs>
1
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93 <param name="lraw" type="data_collection" format="ome.tiff,tiff" collection_type="list" label="Raw Images"/>
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94 <param name="ldfp" type="data_collection" format="ome.tiff,tiff" collection_type="list" optional="true" label="Deep Field Profile Images"/>
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95 <param name="lffp" type="data_collection" format="ome.tiff,tiff" collection_type="list" optional="true" label="Flat Field Profile Images"/>
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96 <param name="flip_x" type="boolean" truevalue="--flip-x" falsevalue="" label="Flip X-axis"/>
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97 <param name="flip_y" type="boolean" truevalue="--flip-y" falsevalue="" label="Flip Y-axis"/>
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98 <param name="max_shift" type="integer" value="30" label="Maximum allowed per-tile corrective shift" help="In micros"/>
4
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99 <conditional name="rename">
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100 <param name="decide" type="select" label="Rename channels in OME-XML metadata">
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101 <option value="do_rename">Rename channels</option>
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102 <option value="dont_rename" selected="true">Leave channel indices</option>
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103 </param>
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104 <when value="do_rename">
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105 <param name="markers_file" type="data" format="csv" label="Markers File"/>
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106 </when>
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107 <when value="dont_rename">
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108 </when>
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109 </conditional>
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110 <section name="adv" title="Advanced Options" expanded="false">
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111 <param name="align_channel" type="integer" value="0" label="Align Channel Number"/>
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112 <param name="stitch_alpha" type="float" optional="true" label="Alpha"/>
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113 <param name="filter_sigma" type="float" optional="true" label="Sigma"/>
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114 <param name="tile_size" type="integer" optional="true" label="Cyto Mask Channel"/>
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115 <param name="flip_mosaic_x" type="boolean" truevalue="--flip-mosaic-x" falsevalue="" label="Flip output image horizontally"/>
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116 <param name="flip_mosaic_y" type="boolean" truevalue="--flip-mosaic-y" falsevalue="" label="Flip output image vertically"/>
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117 </section>
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118 </inputs>
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119
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120 <outputs>
1
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121 <data format="ome.tiff" name="output" from_work_dir="registered.ome.tif" label="${tool.name} on ${on_string}"/>
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122 </outputs>
1
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123 <tests>
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124 <test>
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125 <param name="lraw">
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126 <collection type="list">
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127 <element name="rR1" value="ashlar_test_c0.tiff" />
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128 <element name="rR2" value="ashlar_test_c1.tiff" />
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129 </collection>
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130 </param>
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131 <output name="output" ftype="ome.tiff">
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132 <assert_contents>
3
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133 <has_size value="500000" delta="400000" />
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134 </assert_contents>
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135 </output>
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136 </test>
4
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137 <test>
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138 <param name="lraw">
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139 <collection type="list">
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140 <element name="rR1" value="ashlar_test_c0.tiff" />
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141 <element name="rR2" value="ashlar_test_c1.tiff" />
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142 </collection>
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143 </param>
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144 <conditional name="rename">
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145 <param name="decide" value="do_rename" />
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146 <param name="markers_file" value="ashlar_test_markers.csv" />
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147 </conditional>
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148 <output name="output" ftype="ome.tiff">
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149 <assert_contents>
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150 <has_size value="500000" delta="400000" />
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151 </assert_contents>
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152 </output>
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153 <assert_stdout>
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154 <has_text text="DAPI" />
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155 <has_text text="CD3" />
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156 <has_text text="µm" />
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157 </assert_stdout>
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158 </test>
1
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159 </tests>
0
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160 <help><![CDATA[
1
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161 --------------------------------------------------------------------------------
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162 ASHLAR: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration
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163 --------------------------------------------------------------------------------
0
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164
1
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165 **Whole-slide microscopy image stitching and registration in Python**
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166
1
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167 **Ashlar** performs fast, high-quality stitching of microscopy images. It also
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168 co-registers multiple rounds of cyclic imaging for methods such as CyCIF and
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169 CODEX. Ashlar can read image data directly from BioFormats-supported microscope
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170 vendor file formats as well as a directory of plain TIFF files. Output is saved
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171 as pyramidal, tiled OME-TIFF.
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172
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173 Note that Ashlar requires unstitched individual "tile" images as input, so it is
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174 not suitable for microscopes or slide scanners that only provide pre-stitched
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175 images.
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176
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177 *Visit https://labsyspharm.github.io/ashlar/ for the most up-to-date information on ASHLAR.*
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178 ]]></help>
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179 <expand macro="citations" />
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180 </tool>