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annotate ashlar.xml @ 0:b3054f3d42b2 draft

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"planemo upload for repository https://github.com/ohsu-comp-bio/ashlar commit 27f0c9be58e9e5aecc69067d0e60b5cb945de4b2-dirty"
author perssond
date Fri, 12 Mar 2021 00:14:49 +0000
parents
children f183d9de4622
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1 <tool id="ashlar" name="ASHLAR" version="@VERSION@.6" profile="17.09">
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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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6
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7 <expand macro="requirements"/>
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8 @VERSION_CMD@
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9
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10 <command detect_errors="exit_code"><![CDATA[
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11
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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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14
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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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22
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23 #return $file_clean
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24 #end def
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25
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26 ## Link the illumination files to appropriate file extension
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27 #for $dfp in $ldfp:
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28 ln -s "$dfp" "$clean($dfp,"dfp")" &&
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29 #end for
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30 #for $ffp in $lffp:
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31 ln -s "$ffp" "$clean($ffp,"ffp")" &&
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32 #end for
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33
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34 @CMD_BEGIN@
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35
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36 ## Supply the raw images
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37 #for $raw in $lraw:
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38 "$raw"
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39 #end for
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40
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41 ## Additional arguments
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42 -m $max_shift
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43
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44 #if $flip_x
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45 --flip-x
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46 #end if
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47
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48 #if $flip_y
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49 --flip-y
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50 #end if
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51
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52 -c $adv.align_channel
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53
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54 #if $adv.filter_sigma
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55 --filter-sigma $adv.filter_sigma
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56 #end if
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57
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58 #if $adv.tile_size
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59 --tile-size $adv.tile_size
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60 #end if
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61
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62 --ffp
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63 #for $ffp in $lffp:
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64 "$clean($ffp,"ffp")"
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65 #end for
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66 --dfp
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67 #for $dfp in $ldfp:
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68 "$clean($dfp,"dfp")"
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69 #end for
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70 --pyramid
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71 -f registered.ome.tif;
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72
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73 #if $upgrade.decide == "do_upgrade"
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74 python ${__tool_directory__}/pyramid_upgrade.py
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75 registered.ome.tif
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76
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77 #if $upgrade.markers_file
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78 -n `python "$get_markers" "${upgrade.markers_file}"`
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79 #end if
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80 #end if
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81 ]]></command>
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82
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83 <configfiles>
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84 <configfile name="get_markers">
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85 import pandas as pd
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86 import sys
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87
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88 marker_file = sys.argv[1]
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89 df = pd.read_csv(marker_file)
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90 print(' '.join(df['marker_name'].array))
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91 </configfile>
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92 </configfiles>
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93
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94
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95
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96 <inputs>
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97 <param name="lraw" type="data_collection" format="tiff" collection_type="list" label="Raw Images"/>
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98 <param name="ldfp" type="data_collection" format="tiff" collection_type="list" label="Deep Field Profile Images"/>
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99 <param name="lffp" type="data_collection" format="tiff" collection_type="list" label="Flat Field Profile Images"/>
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100
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101 <param name="flip_x" type="boolean" value="false" label="Flip X-axis"/>
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102 <param name="flip_y" type="boolean" value="false" label="Flip Y-axis"/>
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103
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104 <param name="max_shift" type="integer" value="30" label="Maximum allowed per-tile corrective shift" help="In micros"/>
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105
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106 <conditional name="upgrade">
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107 <param name="decide" type="select" label="Upgrade to BF6-Compliant OME-TIFF Pyramid">
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108 <option value="do_upgrade">Upgrade Pyramid</option>
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109 <option value="dont_upgrade">Leave Legacy Pyramid</option>
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110 </param>
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111 <when value="do_upgrade">
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112 <param name="markers_file" type="data" format="csv,tabular" optional="true" label="Markers File (optional)"/>
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113 </when>
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114 <when value="dont_upgrade">
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115 </when>
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116 </conditional>
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117 <section name="adv" title="Advanced Options" expanded="false">
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118 <param name="align_channel" type="integer" value="0" label="Align Channel Number"/>
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119 <param name="filter_sigma" type="float" optional="true" label="Sigma"/>
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120 <param name="tile_size" type="integer" optional="true" label="Cyto Mask Channel"/>
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121 </section>
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122 </inputs>
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123
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124 <outputs>
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125 <data format="tiff" name="output" from_work_dir="registered.ome.tif" label="${tool.name} on ${on_string}"/>
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126 </outputs>
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127 <help><![CDATA[
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128 Ashlar python package for microscopy registration, developed by HMS (repo: https://github.com/labsyspharm/ashlar)
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129 ashlar [-h] [-o DIR] [-c [CHANNEL]]
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130 [--output-channels [CHANNEL [CHANNEL ...]]] [-m SHIFT]
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131 [--filter-sigma SIGMA] [-f FORMAT] [--pyramid]
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132 [--tile-size PIXELS] [--ffp [FILE [FILE ...]]]
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133 [--dfp [FILE [FILE ...]]] [--plates] [-q] [--version]
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134 [FILE [FILE ...]]
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135
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136 Stitch and align one or more multi-series images
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137
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138 positional arguments:
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139 FILE an image file to be processed (one file per cycle)
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140
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141 optional arguments:
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142 -h, --help show this help message and exit
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143 -o DIR, --output DIR write output image files to DIR; default is the
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144 current directory
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145 -c [CHANNEL], --align-channel [CHANNEL]
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146 align images using channel number CHANNEL; numbering
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147 starts at 0
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148 --output-channels [CHANNEL [CHANNEL ...]]
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149 output only channels listed in CHANNELS; numbering
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150 starts at 0
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151 -m SHIFT, --maximum-shift SHIFT
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152 maximum allowed per-tile corrective shift in microns
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153 --filter-sigma SIGMA width in pixels of Gaussian filter to apply to images
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154 before alignment; default is 0 which disables
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155 filtering
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156 -f FORMAT, --filename-format FORMAT
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157 use FORMAT to generate output filenames, with {cycle}
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158 and {channel} as required placeholders for the cycle
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159 and channel numbers; default is
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160 cycle_{cycle}_channel_{channel}.tif
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161 --pyramid write output as a single pyramidal TIFF
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162 --tile-size PIXELS set tile width and height to PIXELS (pyramid output
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163 only); default is 1024
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164 --ffp [FILE [FILE ...]]
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165 read flat field profile image from FILES; if specified
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166 must be one common file for all cycles or one file for
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167 each cycle
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168 --dfp [FILE [FILE ...]]
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169 read dark field profile image from FILES; if specified
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170 must be one common file for all cycles or one file for
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171 each cycle
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172 --plates enable plate mode for HTS data
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173 -q, --quiet suppress progress display
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174 --version print version
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175
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176 OHSU Wrapper Repo: https://github.com/ohsu-comp-bio/ashlar
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177 Conda Package Available From: https://anaconda.org/ohsu-comp-bio/ashlar
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178 ]]></help>
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179 <expand macro="citations" />
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perssond
parents:
diff changeset
180 </tool>