Mercurial > repos > bgruening > cp_common
annotate starting_modules.xml @ 2:3c3cd68d6d5a draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
author | bgruening |
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date | Thu, 16 Apr 2020 05:29:02 -0400 |
parents | |
children | 27396311a314 |
rev | line source |
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2
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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1 <tool id="cp_common" name="Starting modules" version="@CP_VERSION@"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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2 <description>load images and metadata into CellProfiler (Images, Metadata, NamesAndTypes, Groups)</description> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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3 <macros> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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4 <import>macros.xml</import> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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5 <xml name="image_type_condition"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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6 <conditional name="con_set_intensity"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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7 <param name="set_intensity_range_from" type="select" label="Set intensity range from"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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8 <option value="Image metadata">Image metadata</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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9 <option value="Image bit-depth">Image bit-depth</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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10 <option value="Manual">Manual</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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11 </param> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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12 <when value="Manual"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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13 <param name="maximum_intensity" type="float" value="255.0" label="Maximum intensity"/> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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14 </when> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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15 <when value="Image metadata" /> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
16 <when value="Image bit-depth" /> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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17 </conditional> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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18 </xml> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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19 <xml name="name_type_rule_matching_file"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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20 <param name="operator" type="select"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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21 <option value="does">Does</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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22 <option value="doesnot">Does not</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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23 </param> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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24 <param name="contain" type="select"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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25 <option value="contain">Contain</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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26 <option value="Contain regular expression">Contain regular expression</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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27 <option value="startwith">Start with</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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28 <option value="endwith">End with</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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29 <option value="Exactly match">Exactly match</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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30 </param> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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31 <param name="match_value" type="text"/> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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32 </xml> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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33 <xml name="image_matching_rules"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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34 <repeat name="r_match_rule" title="Rules"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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35 <param name="match_all_any" type="select" display="radio" label="Match the following rules"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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36 <option value="and">All</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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37 <option value="or">Any</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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38 </param> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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39 <conditional name="con_match"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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40 <param name="rule_type" type="select" label="Select rule criteria"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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41 <option value="file">File</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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42 <option value="directory">Directory</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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43 <option value="extension">Extension</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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44 <option value="image">Image</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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45 <option value="metadata">Metadata</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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46 </param> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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47 <when value="file"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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48 <expand macro="name_type_rule_matching_file"/> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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49 </when> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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50 <when value="directory"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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51 <expand macro="name_type_rule_matching_file"/> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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52 </when> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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53 <when value="extension" /> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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54 <when value="image"/> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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55 <when value="metadata"/> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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56 </conditional> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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57 <param name="name_to_assign" label="Name to assign these images" type="text" /> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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58 <conditional name="con_select_image_type"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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59 <param name="select_image_type" type="select" label="Select the image type"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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60 <option value="Grayscale image">Grayscale image</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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61 <option value="Color image">Color image</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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62 <option value="Binary mask">Binary mask</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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63 </param> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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64 <when value ="Grayscale image"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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65 <expand macro="image_type_condition" /> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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66 </when> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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67 <when value="Color image"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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68 <expand macro="image_type_condition" /> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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69 </when> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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70 <when value="Binary mask"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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71 </when> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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72 </conditional> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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73 </repeat> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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74 </xml> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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75 </macros> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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76 <expand macro="py_requirements"/> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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77 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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78 <command detect_errors="aggressive"><![CDATA[ |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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79 python '$script_file' '$inputs' |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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80 ]]></command> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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81 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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82 <configfiles> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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83 <inputs name="inputs"/> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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84 <configfile name="script_file"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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85 import json |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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86 import sys |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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87 import os |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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88 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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89 FOURSPACES = @SPACES@ |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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90 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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91 input_json_path = sys.argv[1] |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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92 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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93 params = json.load(open(input_json_path, "r")) |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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94 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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95 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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96 def write_images(): |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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97 filter_images = params['images']['filter_images'] |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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98 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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99 _str = "\nImages:[module_num:1|svn_version:\\'Unknown\\'|variable_revision_number:2|show_window:False|notes:\\x5B\\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n" |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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100 _str += FOURSPACES+":\n" |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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101 _str += FOURSPACES + "Filter images?:%s\n" % filter_images |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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102 _str += FOURSPACES + "Select the rule criteria:and (extension does isimage) (directory doesnot startwith \".\")\n" |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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103 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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104 return _str |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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105 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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106 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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107 def write_metadata(): |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
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108 metadata_extraction = params['metadata']['con_metadata_extraction'] |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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109 extract = metadata_extraction['extract'] |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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110 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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changeset
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111 if 'extraction_method' in metadata_extraction: |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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112 method_count = len(metadata_extraction['extraction_method']) |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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113 else: |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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114 method_count = 1 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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changeset
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115 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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116 _str = "\nMetadata:[module_num:2|svn_version:\\'Unknown\\'|variable_revision_number:4|show_window:False|notes:\\x5B\\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n" |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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117 _str += FOURSPACES + "Extract metadata?:%s\n" % extract |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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118 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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119 if extract == "No": |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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120 _str += FOURSPACES + "Metadata data type:Text\n" |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
121 _str += FOURSPACES + "Metadata types:{}\n" |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
122 _str += FOURSPACES + "Extraction method count:%d\n" % method_count |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
123 _str += FOURSPACES + "Metadata extraction method:Extract from file/folder names\n" |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
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124 _str += FOURSPACES + "Regular expression to extract from file name:^(?P<Plate>.*)_(?P<Well>\x5BA-P\x5D\x5B0-9\x5D{2})_s(?P<Site>\x5B0-9\x5D)_w(?P<ChannelNumber>\x5B0-9\x5D)\n" |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
125 _str += FOURSPACES + "Regular expression to extract from folder name:(?P<Date>\x5B0-9\x5D{4}_\x5B0-9\x5D{2}_\x5B0-9\x5D{2})$\n" |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
126 _str += FOURSPACES + "Extract metadata from:All images\n" |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
127 _str += FOURSPACES + "Select the filtering criteria:and (file does contain \"\")\n" |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
128 _str += FOURSPACES + "Metadata file location:\n" |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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129 _str += FOURSPACES + "Match file and image metadata:\x5B\x5D\n" |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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|
130 _str += FOURSPACES + "Use case insensitive matching?:No\n" |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
131 else: |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
132 _str += FOURSPACES + "Metadata data type:%s\n" % metadata_extraction['metadata_type'] |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
133 _str += FOURSPACES + "Metadata types:{}\n" |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
134 _str += FOURSPACES + "Extraction method count:%d\n" % method_count |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
135 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
136 for methods in metadata_extraction["extraction_method"]: |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
137 _str += FOURSPACES + "Metadata extraction method:%s\n" % methods["metadata_extraction_method"] |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
138 _str += FOURSPACES + "Metadata source:%s\n" % methods["metadata_source"] |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
139 _str += FOURSPACES + "Regular expression to extract from file name:%s\n" % methods["file_name_regex"] |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
140 _str += FOURSPACES + "Regular expression to extract from folder name:%s\n" % methods["folder_name_regex"] |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
141 _str += FOURSPACES + "Extract metadata from:%s\n" % methods["extract_metadata_from"] |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
142 _str += FOURSPACES + "Select the filtering criteria:and (file does contain \"\")\n" |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
143 _str += FOURSPACES + "Metadata file location:\n" |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
144 _str += FOURSPACES + "Match file and image metadata:\x5B\x5D\n" |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
145 _str += FOURSPACES + "Use case insensitive matching?:No\n" |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
146 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
147 return _str |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
148 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
149 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
150 def write_nameandtypes(): |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
151 nameandtypes = params['nameandtypes'] |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
152 assign_a_name = nameandtypes['con_assign_a_name_to']['assign_a_name_to'] |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
153 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
154 if "con_select_image_type" in nameandtypes['con_assign_a_name_to']: |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
155 con_set_intensity = nameandtypes['con_assign_a_name_to']['con_select_image_type']['con_set_intensity'] |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
156 max_intensity = con_set_intensity['maximum_intensity'] if "maximum_intensity" in con_set_intensity else 255.0 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
157 else: |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
158 max_intensity = 255.0 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
159 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
160 pixel_space = nameandtypes['pixel_space'] |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
161 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
162 rule_count = len(nameandtypes['r_match_rule']) if "r_match_rule" in nameandtypes else 1 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
163 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
164 process_3d = nameandtypes['pixel_space']['process_3d'] |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
165 x_spacing = 1.0 if "x_spacing" not in pixel_space else pixel_space["x_spacing"] |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
166 y_spacing = 1.0 if "y_spacing" not in pixel_space else pixel_space["y_spacing"] |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
167 z_spacing = 1.0 if "z_spacing" not in pixel_space else pixel_space["z_spacing"] |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
168 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
169 _str = "\nNamesAndTypes:[module_num:3|svn_version:\\'Unknown\\'|variable_revision_number:8|show_window:False|notes:\\x5B\\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\\'\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n" |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
170 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
171 _str += FOURSPACES + "Assign a name to:%s\n" % assign_a_name |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
172 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
173 if assign_a_name == "All images": |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
174 _str += FOURSPACES + "Select the image type:%s\n" % nameandtypes['con_assign_a_name_to']['con_select_image_type']['select_image_type'] |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
175 _str += FOURSPACES + "Name to assign these images:%s\n" % nameandtypes['con_assign_a_name_to']['name_to_assign'] |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
176 _str += FOURSPACES + "Match metadata:[]\n" |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
177 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
178 _str += FOURSPACES + "Image set matching method:Order\n" |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
179 _str += FOURSPACES + "Set intensity range from:%s\n" % con_set_intensity['set_intensity_range_from'] |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
180 _str += FOURSPACES + "Assignments count:%s\n" % rule_count |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
181 _str += FOURSPACES + "Single images count:0\n" |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
182 _str += FOURSPACES + "Maximum intensity:%.1f\n" % max_intensity |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
183 _str += FOURSPACES + "Process as 3D?:%s\n" % process_3d |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
184 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
185 _str += FOURSPACES + "Relative pixel spacing in X:%.1f\n" % x_spacing |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
186 _str += FOURSPACES + "Relative pixel spacing in Y:%.1f\n" % y_spacing |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
187 _str += FOURSPACES + "Relative pixel spacing in Z:%.1f\n" % z_spacing |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
188 else: |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
189 _str += FOURSPACES + "Select the image type:Grayscale image\n" |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
190 _str += FOURSPACES + "Name to assign these images:DNA\n" |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
191 _str += FOURSPACES + "Match metadata:[]\n" |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
192 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
193 _str += FOURSPACES + "Image set matching method:%s\n" % nameandtypes['con_assign_a_name_to']['matching_method'] |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
194 _str += FOURSPACES + "Set intensity range from:Image metadata\n" |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
195 _str += FOURSPACES + "Assignments count:%d\n" % rule_count |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
196 _str += FOURSPACES + "Single images count:0\n" |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
197 _str += FOURSPACES + "Maximum intensity:%.1f\n" % max_intensity |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
198 _str += FOURSPACES + "Process as 3D?:%s\n" % process_3d |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
199 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
200 _str += FOURSPACES + "Relative pixel spacing in X:1.0\n" |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
201 _str += FOURSPACES + "Relative pixel spacing in Y:1.0\n" |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
202 _str += FOURSPACES + "Relative pixel spacing in Z:1.0\n" |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
203 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
204 for rule in nameandtypes["con_assign_a_name_to"]["r_match_rule"]: |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
205 _str += FOURSPACES + "Select the rule criteria:%s%s%s%s%s%s%s%s%s%s\n" % (rule["match_all_any"], " (",rule["con_match"]["rule_type"], " ",rule["con_match"]["operator"]," ",rule["con_match"]["contain"]," \"",rule["con_match"]["match_value"],"\")") |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
206 _str += FOURSPACES + "Name to assign these images:%s\n" % rule["name_to_assign"] |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
207 _str += FOURSPACES + "Name to assign these objects:Cell\n" |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
208 _str += FOURSPACES + "Select the image type:%s\n" % rule["con_select_image_type"]["select_image_type"] |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
209 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
210 intensity_range = rule["con_select_image_type"]["con_set_intensity"]["set_intensity_range_from"] |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
211 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
212 _str += FOURSPACES + "Set intensity range from:%s\n" % intensity_range |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
213 _str += FOURSPACES + "Select the image type:%s\n" % rule["con_select_image_type"]["select_image_type"] |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
214 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
215 if intensity_range == "Manual": |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
216 _str += FOURSPACES + "Maximum intensity:%s\n" % rule["con_select_image_type"]["con_set_intensity"]["maximum_intensity"] |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
217 else: |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
218 _str += FOURSPACES + "Maximum intensity:255.0\n" |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
219 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
220 if process_3d == "Yes": |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
221 _str += FOURSPACES + "Relative pixel spacing in X:%.1f\n" % x_spacing |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
222 _str += FOURSPACES + "Relative pixel spacing in Y:%.1f\n" % y_spacing |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
223 _str += FOURSPACES + "Relative pixel spacing in Z:%.1f\n" % z_spacing |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
224 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
225 return _str |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
226 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
227 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
228 def write_groups(): |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
229 groups = params['groups'] |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
230 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
231 _str = "\nGroups:[module_num:4|svn_version:\\'Unknown\\'|variable_revision_number:2|show_window:False|notes:\\x5B\\\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\\'\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n" |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
232 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
233 _str += FOURSPACES + "Do you want to group your images?:%s\n" % groups["con_groups"]["group_images"] |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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234 _str += FOURSPACES + "grouping metadata count:1\n" |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
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235 _str += FOURSPACES + "Metadata category:%s\n" % groups["con_groups"]["group_category"] |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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236 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
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237 return _str |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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238 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
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239 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
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240 with open("output", "w") as f: |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
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241 headers = ["CellProfiler Pipeline: http://www.cellprofiler.org\n", |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
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242 "Version:3\n", |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
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243 "DateRevision:319\n", |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
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244 "GitHash:\n", |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
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245 "ModuleCount:4\n", |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
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246 "HasImagePlaneDetails:False", |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
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247 "\n"] |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
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248 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
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249 f.writelines(headers) |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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250 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
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251 img_str = write_images() |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
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252 metadata_str = write_metadata() |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
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253 nameandtypes_str = write_nameandtypes() |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
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254 groups_str = write_groups() |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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255 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
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256 output_str = img_str + metadata_str + nameandtypes_str + groups_str |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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257 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
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258 f.write(output_str) |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
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259 f.close() |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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260 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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261 </configfile> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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262 </configfiles> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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263 <inputs> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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264 <!-- Images module--> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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265 <section name="images" title="Images" expanded="false"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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266 <param name="filter_images" type="select" label="Filter images?"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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267 <option value="Images only">Images only</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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268 <option value="No filtering">No filtering</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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269 </param> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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270 </section> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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271 <!-- Metadata module--> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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272 <section name="metadata" title="Metadata" expanded="false"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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273 <conditional name="con_metadata_extraction"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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274 <param name="extract" type="select" display="radio" label="Extract metadata?"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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275 <option value="No">No</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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276 <option value="Yes">Yes</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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277 </param> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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278 <when value="Yes"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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279 <repeat name="extraction_method" title="metadata"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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|
280 <param name="metadata_extraction_method" type="select" label="Metadata extraction method"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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281 <option value="Extract from file/folder names">Extract from file/folder names</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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282 <option value="Import from file">Import from file</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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|
283 <option value="Extract from image file headers">Extract from image file headers</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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|
284 </param> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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285 <param name="metadata_source" type="select" label="Metadata source"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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286 <option value="File name">File name</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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|
287 <option value="Folder name">Folder name</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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288 </param> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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289 <param name="file_name_regex" type="select" label="Select file name pattern to extract from file name" help="Image file names must comply with one of the patterns.For example, AS_09125_050116030001_D03f00d0.tif matches the pattern field1_filed2_field3_field4. If none of the patterns are suitable, please use other Galaxy tools to rename your files first. "> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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|
290 <sanitizer sanitize="false"/> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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|
291 <option value="(?P<field1>.*)">field1</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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|
292 <option value="(?P<field1>.*)-(?P<field2>[a-zA-Z0-9]+)">field1-field2</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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293 <option value="(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)">field1_field2</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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294 <option value="(?P<field1>.*)__(?P<field2>[a-zA-Z0-9]+)">field1__field2</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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295 <option value="(?P<field1>.*)-(?P<field2>[a-zA-Z0-9]+)-(?P<field3>[a-zA-Z0-9]+)">field1-field2-field3</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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296 <option value="(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)">field1_field2_field3</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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|
297 <option value="(?P<field1>.*)__(?P<field2>[a-zA-Z0-9]+)__(?P<field3>[a-zA-Z0-9]+)">field1__field2__field3</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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298 <option value="(?P<field1>.*)-(?P<field2>[a-zA-Z0-9]+)-(?P<field3>[a-zA-Z0-9]+)-(?P<field4>[a-zA-Z0-9]+)">field1-field2-field3-field4</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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299 <option value="(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)">field1_field2_field3_field4</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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|
300 <option value="(?P<field1>.*)__(?P<field2>[a-zA-Z0-9]+)__(?P<field3>[a-zA-Z0-9]+)__(?P<field4>[a-zA-Z0-9]+)">field1__field2__field3__field4</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
301 <option value="(?P<field1>.*)-(?P<field2>[a-zA-Z0-9]+)-(?P<field3>[a-zA-Z0-9]+)-(?P<field4>[a-zA-Z0-9]+)-(?P<field5>[a-zA-Z0-9]+)">field1-field2-field3-field4-field5</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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|
302 <option value="(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)_(?P<field5>[a-zA-Z0-9]+)">field1_field2_field3_field4_field5</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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|
303 <option value="(?P<field1>.*)__(?P<field2>[a-zA-Z0-9]+)__(?P<field3>[a-zA-Z0-9]+)__(?P<field4>[a-zA-Z0-9]+)__(?P<field5>[a-zA-Z0-9]+)">field1__field2__field3__field4__field5</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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304 <option value="(?P<field1>.*)-(?P<field2>[a-zA-Z0-9]+)-(?P<field3>[a-zA-Z0-9]+)-(?P<field4>[a-zA-Z0-9]+)-(?P<field5>[a-zA-Z0-9]+)-(?P<field6>[a-zA-Z0-9]+)">field1-field2-field3-field4-field5-field6</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
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|
305 <option value="(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)_(?P<field5>[a-zA-Z0-9]+)_(?P<field6>[a-zA-Z0-9]+)">field1_field2_field3_field4_field5_field6</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
306 <option value="(?P<field1>.*)__(?P<field2>[a-zA-Z0-9]+)__(?P<field3>[a-zA-Z0-9]+)__(?P<field4>[a-zA-Z0-9]+)__(?P<field5>[a-zA-Z0-9]+)__(?P<field6>[a-zA-Z0-9]+)">field1__field2__field3__field4__field5__field6</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
307 </param> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
308 <param name="folder_name_regex" type="select" label="Select folder name pattern to extract from folder name" help="Folder names must comply with one of the patterns.For example, folder name images-exp1 matches the pattern field1-field2. If none of the patterns are suitable, please use other Galaxy tools to rename your folder first. "> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
309 <sanitizer sanitize="false"/> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
310 <option value="(?P<field1>.*)">field1</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
311 <option value="(?P<field1>.*)-(?P<field2>[a-zA-Z0-9]+)">field1-field2</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
312 <option value="(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)">field1_field2</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
313 </param> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
314 <param name="extract_metadata_from" type="select" label="Extract metadata from"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
315 <option value="All images">All images</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
316 <option value="Images matching a rule">Images matching a rule</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
317 </param> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
318 </repeat> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
319 <param name="metadata_type" type="select" label="Metadata data type"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
320 <option value="Text">Text</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
321 </param> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
322 </when> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
323 <when value="No"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
324 </when> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
325 </conditional> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
326 </section> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
327 <!-- NamesAndTypes--> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
328 <section name="nameandtypes" title="NamesAndTypes" expanded="false"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
329 <conditional name="pixel_space"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
330 <param name="process_3d" type="select" display="radio" label="Process 3D"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
331 <option value="No">No</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
332 <option value="Yes">Yes</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
333 </param> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
334 <when value="Yes"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
335 <param name="x_spacing" type="float" value="1.0" label="Relative pixel spacing in X"/> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
336 <param name="y_spacing" type="float" value="1.0" label="Relative pixel spacing in Y"/> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
337 <param name="z_spacing" type="float" value="1.0" label="Relative pixel spacing in Z"/> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
338 </when> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
339 <when value="No"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
340 </when> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
341 </conditional> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
342 <conditional name="con_assign_a_name_to"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
343 <param name="assign_a_name_to" type="select" label="Assign a name to"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
344 <option value="All images">All images</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
345 <option value="Images matching rules">Images matching rules</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
346 </param> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
347 <when value="All images"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
348 <param name="name_to_assign" type="text" value="DNA" label="Name to assign these images"/> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
349 <conditional name="con_select_image_type"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
350 <param name="select_image_type" type="select" label="Select the image type"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
351 <option value="Grayscale image">Grayscale image</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
352 <option value="Color image">Color image</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
353 <option value="Binary mask">Binary mask</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
354 </param> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
355 <when value ="Grayscale image"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
356 <expand macro="image_type_condition" /> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
357 </when> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
358 <when value="Color image"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
359 <expand macro="image_type_condition" /> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
360 </when> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
361 <when value="Binary mask"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
362 </when> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
363 </conditional> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
364 </when> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
365 <when value="Images matching rules"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
366 <expand macro="image_matching_rules"/> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
367 <param name="matching_method" type="select" label="Image set matching method"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
368 <option value="Order">Order</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
369 <option value="Metadata">Metadata</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
370 </param> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
371 </when> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
372 </conditional> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
373 </section> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
374 <!-- Groups --> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
375 <section name="groups" title="Groups" expanded="false"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
376 <conditional name="con_groups"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
377 <param name="group_images" type="select" value="No" label="Do you want to group your images?" display="radio"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
378 <option value="Yes">Yes</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
379 <option value="No">No</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
380 </param> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
381 <when value="Yes"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
382 <param name="group_category" type="select" label="Metadata category"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
383 <option value="FileLocation">FileLocation</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
384 <option value="Frame">Frame</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
385 <option value="ImageId">ImageId</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff
changeset
|
386 <option value="Screen">Screen</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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387 <option value="Series">Series</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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388 <option value="field1">field1</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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389 <option value="field2">field2</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
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390 <option value="field3">field3</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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391 <option value="field4">field4</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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392 <option value="field5">field5</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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393 <option value="field6">field6</option> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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394 </param> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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395 </when> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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396 <when value="No"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
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397 </when> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
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398 </conditional> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
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399 </section> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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400 </inputs> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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401 <outputs> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
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402 <expand macro="output_pipeline_macro" /> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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403 </outputs> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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|
404 <tests> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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405 <test> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
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406 <param name="filter_images" value="Images only"/> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
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407 <conditional name="con_metadata_extraction"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
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408 <param name="extract" value="Yes"/> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
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409 <repeat name="extraction_method"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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410 <param name="metadata_extraction_method" value="Extract from file/folder names"/> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
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411 <param name="metadata_source" value="File name" /> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
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412 <param name="file_name_regex" value="(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)" /> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
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413 <param name="extract_metadata_from" value="All images" /> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
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414 </repeat> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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415 <param name="metadata_type" value="Text" /> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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416 </conditional> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
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417 <conditional name="pixel_space"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
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418 <param name="process_3d" value="No"/> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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419 </conditional> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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420 <conditional name="con_assign_a_name_to"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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421 <param name="assign_a_name_to" value="Images matching rules"/> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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|
422 <repeat name="r_match_rule"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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|
423 <param name="match_all_any" value="and" /> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
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424 <conditional name="con_match"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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|
425 <param name="rule_type" value="file" /> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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|
426 <param name="operator" value="does" /> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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|
427 <param name="contain" value="startwith" /> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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428 <param name="match_value" value="im" /> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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429 </conditional> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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430 <param name="name_to_assign" value="DNA" /> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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431 <conditional name="con_select_image_type"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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432 <param name="select_image_type" value="Grayscale image" /> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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|
433 <conditional name="con_set_intensity"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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434 <param name="set_intensity_range_from" value="Image metadata" /> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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435 </conditional> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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|
436 </conditional> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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437 </repeat> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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438 <param name="matching_method" value="Order" /> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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|
439 </conditional> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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|
440 <conditional name="con_groups"> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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441 <param name="group_images" value="Yes" /> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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442 <param name="group_category" value="Screen" /> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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443 </conditional> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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444 <expand macro="test_out_file" /> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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parents:
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445 </test> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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446 </tests> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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|
447 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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448 <help> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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449 This tool builds a CellProfiler pipeline file with headers and 4 compulsory modules, 'Images', 'Metadata', 'NamesAndTypes' and 'Groups'. |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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parents:
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450 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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451 No input parameters are needed for this tool. The rest CP modules will build based on the output of this file. |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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parents:
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452 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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|
453 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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454 Images: use the Images module to compile a list of files that you want to analyze. |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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parents:
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455 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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456 Metadata: optionally allows you to extract information describing your images (i.e., metadata) which will be stored along with your measurements. |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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|
457 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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458 NamesAndTypes: allows you to assign a meaningful name to each image by which other modules will refer to it. |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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parents:
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|
459 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
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460 Groups: optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc. |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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|
461 |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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462 </help> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
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463 <expand macro="citations" /> |
3c3cd68d6d5a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
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464 </tool> |