Mercurial > repos > iuc > cialign
annotate cialign.xml @ 1:3c5bdab3c7b7 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit 4272ec0a9c9fc6c2a54aa702a3dc446ec598ffcc
| author | iuc |
|---|---|
| date | Tue, 05 Aug 2025 20:08:31 +0000 |
| parents | c0a3b4607e66 |
| children |
| rev | line source |
|---|---|
|
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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1 <tool id="cialign" name="CIAlign" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.2"> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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2 <description>clean, visualise and analyse a multiple sequence alignment</description> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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3 <macros> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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4 <import>macros.xml</import> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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5 </macros> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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6 <expand macro="requirements"/> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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7 <version_command>CIAlign --version</version_command> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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8 <command detect_errors="exit_code"><![CDATA[ |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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9 #if str($input.extension) == "fasta.gz": |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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10 gunzip -c '$input' > input.fasta && |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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11 CIAlign --infile input.fasta |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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12 #else: |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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13 CIAlign --infile '$input' |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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14 #end if |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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15 --outfile_stem 'output' |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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16 |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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17 ###### Basic Options |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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18 $basic_options.all |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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19 $basic_options.clean |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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20 $basic_options.visualise |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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21 $basic_options.interpret |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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22 |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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23 ###### Cleaning Options |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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24 ### Remove Divergent options |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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25 #if str($cleaning_options.remove_divergent_cond.remove_divergent_param) == "true": |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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26 --remove_divergent |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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27 --remove_divergent_minperc $cleaning_options.remove_divergent_cond.remove_divergent_minperc |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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28 #for $s in $cleaning_options.remove_divergent_cond.remove_divergent_retain_seqs |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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29 --remove_divergent_retain '$s.remove_divergent_retain' |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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30 #end for |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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31 #for $s in $cleaning_options.remove_divergent_cond.remove_divergent_retain_strings |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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32 --remove_divergent_retain_str '$s.remove_divergent_retain_str' |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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33 #end for |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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34 #end if |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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35 |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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36 ### Remove Insertions options |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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37 #if str($cleaning_options.remove_insertions_cond.remove_insertions_param) == "true": |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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38 --remove_insertions |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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39 --insertion_min_size $cleaning_options.remove_insertions_cond.insertion_min_size |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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40 --insertion_max_size $cleaning_options.remove_insertions_cond.insertion_max_size |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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41 --insertion_min_flank $cleaning_options.remove_insertions_cond.insertion_min_flank |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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42 --insertion_min_perc $cleaning_options.remove_insertions_cond.insertion_min_perc |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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43 #end if |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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44 |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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45 ### Crop Ends options |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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46 #if str($cleaning_options.crop_ends_cond.crop_ends_param) == "true": |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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47 --crop_ends |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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48 --crop_ends_mingap_perc $cleaning_options.crop_ends_cond.crop_ends_mingap_perc |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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49 --crop_ends_redefine_perc $cleaning_options.crop_ends_cond.crop_ends_redefine_perc |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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50 #for $s in $cleaning_options.crop_ends_cond.crop_ends_retain_seqs |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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51 --crop_ends_retain '$s.crop_ends_retain' |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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52 #end for |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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53 #for $s in $cleaning_options.crop_ends_cond.crop_ends_retain_strings |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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54 --crop_ends_retain_str '$s.crop_ends_retain_str' |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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55 #end for |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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56 #end if |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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57 |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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58 ### Remove Short options |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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59 #if str($cleaning_options.remove_short_cond.remove_short_param) == "true": |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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60 --remove_short |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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61 --remove_min_length $cleaning_options.remove_short_cond.remove_min_length |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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62 #for $s in $cleaning_options.remove_short_cond.remove_short_retain_seqs |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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63 --remove_short_retain '$s.remove_short_retain' |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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64 #end for |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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65 #for $s in $cleaning_options.remove_short_cond.remove_short_retain_strings |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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66 --remove_short_retain_str '$s.remove_short_retain_str' |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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67 #end for |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
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68 #end if |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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69 |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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70 ### Crop Divergent options |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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71 #if str($cleaning_options.crop_divergent_cond.crop_divergent_param) == "true": |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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72 --crop_divergent |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
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73 --crop_divergent_min_prop_ident $cleaning_options.crop_divergent_cond.crop_divergent_min_prop_ident |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
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74 --crop_divergent_min_prop_nongap $cleaning_options.crop_divergent_cond.crop_divergent_min_prop_nongap |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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75 --crop_divergent_buffer_size $cleaning_options.crop_divergent_cond.crop_divergent_buffer_size |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
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76 #end if |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
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77 |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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changeset
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78 ### Retain options |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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79 #if str($cleaning_options.retain_cond.retain_param) == "true": |
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c0a3b4607e66
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80 #for $s in $cleaning_options.retain_cond.retain_seqs |
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c0a3b4607e66
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81 --retain '$s.retain' |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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parents:
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changeset
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82 #end for |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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83 #for $s in $cleaning_options.retain_cond.retain_strings |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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84 --retain_str '$s.retain_str' |
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c0a3b4607e66
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parents:
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85 #end for |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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86 #end if |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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87 |
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c0a3b4607e66
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88 ### Keep Gap only |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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89 $cleaning_options.keep_gaponly |
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c0a3b4607e66
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90 |
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c0a3b4607e66
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91 ###### Visualisation Options |
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c0a3b4607e66
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92 ### basic visualisation options |
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c0a3b4607e66
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93 $visualisation_options.basic_visualisation_options.plot_input |
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c0a3b4607e66
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94 $visualisation_options.basic_visualisation_options.plot_output |
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c0a3b4607e66
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95 $visualisation_options.basic_visualisation_options.plot_markup |
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c0a3b4607e66
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96 $visualisation_options.basic_visualisation_options.plot_consensus_identity |
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c0a3b4607e66
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97 $visualisation_options.basic_visualisation_options.plot_consensus_similarity |
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c0a3b4607e66
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98 #if str($visualisation_options.output_settings_cond.output_settings_param) == "true": |
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c0a3b4607e66
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99 --plot_width $visualisation_options.basic_visualisation_options.output_settings_cond.plot_width |
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c0a3b4607e66
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100 --plot_height $visualisation_options.basic_visualisation_options.output_settings_cond.plot_height |
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c0a3b4607e66
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101 --plot_dpi $visualisation_options.basic_visualisation_options.output_settings_cond.plot_dpi |
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c0a3b4607e66
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102 $visualisation_options.basic_visualisation_options.output_settings_cond.plot_keep_numbers |
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c0a3b4607e66
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103 $visualisation_options.basic_visualisation_options.output_settings_cond.plot_force_numbers |
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c0a3b4607e66
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104 --plot_identity_palette '$visualisation_options.basic_visualisation_options.output_settings_cond.plot_identity_palette' |
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c0a3b4607e66
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105 --plot_identity_gap_col '$visualisation_options.basic_visualisation_options.output_settings_cond.plot_identity_gap_col' |
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c0a3b4607e66
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106 --plot_similarity_palette '$visualisation_options.basic_visualisation_options.output_settings_cond.plot_similarity_palette' |
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c0a3b4607e66
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107 --plot_similarity_gap_col '$visualisation_options.basic_visualisation_options.output_settings_cond.plot_similarity_gap_col' |
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c0a3b4607e66
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108 --plot_sub_matrix_name '$visualisation_options.basic_visualisation_options.output_settings_cond.plot_sub_matrix_name' |
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c0a3b4607e66
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109 --palette '$visualisation_options.basic_visualisation_options.output_settings_cond.palette' |
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c0a3b4607e66
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110 #end if |
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c0a3b4607e66
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111 |
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c0a3b4607e66
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112 ### Sequence logos |
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c0a3b4607e66
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113 #if str($visualisation_options.sequence_logo_cond.sequence_logo_param) == "true": |
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c0a3b4607e66
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114 --make_sequence_logo |
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c0a3b4607e66
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115 --sequence_logo_type "$visualisation_options.sequence_logo_cond.sequence_logo_type" |
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c0a3b4607e66
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116 --sequence_logo_dpi $visualisation_options.sequence_logo_cond.sequence_logo_dpi |
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c0a3b4607e66
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117 --sequence_logo_font '$visualisation_options.sequence_logo_cond.sequence_logo_font' |
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c0a3b4607e66
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118 --sequence_logo_nt_per_row $visualisation_options.sequence_logo_cond.sequence_logo_nt_per_row |
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c0a3b4607e66
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119 #if $visualisation_options.sequence_logo_cond.logo_start: |
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c0a3b4607e66
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120 --logo_start $visualisation_options.sequence_logo_cond.logo_start |
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c0a3b4607e66
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121 #end if |
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c0a3b4607e66
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122 #if $visualisation_options.sequence_logo_cond.logo_end: |
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c0a3b4607e66
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123 --logo_end $visualisation_options.sequence_logo_cond.logo_end |
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c0a3b4607e66
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124 #end if |
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c0a3b4607e66
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125 #end if |
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c0a3b4607e66
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126 |
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c0a3b4607e66
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127 ### Statistics Plots |
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c0a3b4607e66
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128 $visualisation_options.statistics_plots.plot_stats_input |
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c0a3b4607e66
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129 $visualisation_options.statistics_plots.plot_stats_output |
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130 #if $visualisation_options.statistics_plots.plot_stats_input or $visualisation_options.statistics_plots.plot_stats_output |
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131 --plot_stats_dpi $visualisation_options.statistics_plots.stats_settings.plot_stats_dpi |
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132 --plot_stats_height $visualisation_options.statistics_plots.stats_settings.plot_stats_width |
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133 --plot_stats_width $visualisation_options.statistics_plots.stats_settings.plot_stats_height |
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134 --plot_stats_colour '$visualisation_options.statistics_plots.stats_settings.plot_stats_colour' |
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135 #end if |
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c0a3b4607e66
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136 |
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c0a3b4607e66
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137 ###### Interpretation Functions |
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c0a3b4607e66
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138 ### consensus sequences |
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c0a3b4607e66
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139 #if str($interpretation_options.consensus_sequences_cond.consensus_sequences_param) == "true": |
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140 --make_consensus |
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c0a3b4607e66
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141 --consensus_type '$interpretation_options.consensus_sequences_cond.consensus_type' |
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c0a3b4607e66
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142 $interpretation_options.consensus_sequences_cond.consensus_keep_gaps |
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143 #end if |
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144 |
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c0a3b4607e66
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145 ### Position Matrices |
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c0a3b4607e66
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146 $interpretation_options.position_matrices.pwm_input |
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c0a3b4607e66
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147 $interpretation_options.position_matrices.pwm_output |
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c0a3b4607e66
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148 #if $interpretation_options.position_matrices.matrices_settings.pwm_start: |
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149 --pwm_start $interpretation_options.position_matrices.matrices_settings.pwm_start |
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c0a3b4607e66
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150 #end if |
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c0a3b4607e66
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151 #if $interpretation_options.position_matrices.matrices_settings.pwm_end: |
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c0a3b4607e66
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152 --pwm_end $interpretation_options.position_matrices.matrices_settings.pwm_end |
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c0a3b4607e66
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153 #end if |
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c0a3b4607e66
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154 #if $interpretation_options.position_matrices.pwm_input or $interpretation_options.position_matrices.pwm_output: |
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155 --pwm_freqtype '$interpretation_options.position_matrices.matrices_settings.pwm_freqtype' |
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156 --pwm_alphatype '$interpretation_options.position_matrices.matrices_settings.pwm_alphatype' |
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157 --pwm_alphaval $interpretation_options.position_matrices.matrices_settings.pwm_alphaval |
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158 #end if |
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159 $interpretation_options.position_matrices.pwm_output_blamm |
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160 $interpretation_options.position_matrices.pwm_output_meme |
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161 |
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162 ### Similarity Matrices |
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163 $interpretation_options.similarity_matrices.make_similarity_matrix_input |
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164 $interpretation_options.similarity_matrices.make_similarity_matrix_output |
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165 #if $interpretation_options.similarity_matrices.make_similarity_matrix_input or $interpretation_options.similarity_matrices.make_similarity_matrix_output: |
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166 --make_simmatrix_keepgaps $interpretation_options.similarity_matrices.similarity_matrices_settings.make_simmatrix_keepgaps |
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167 --make_simmatrix_dp $interpretation_options.similarity_matrices.similarity_matrices_settings.make_simmatrix_dp |
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168 --make_simmatrix_minoverlap $interpretation_options.similarity_matrices.similarity_matrices_settings.make_simmatrix_minoverlap |
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169 #end if |
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170 |
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171 |
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172 ###### Editing Functions |
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173 #if str($editing_functions.get_section_cond.get_section_param) == "true": |
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174 --get_section |
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175 --section_start $editing_functions.get_section_cond.section_start |
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176 --section_end $editing_functions.get_section_cond.section_end |
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177 #end if |
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178 $editing_functions.replace_input_tu |
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179 $editing_functions.replace_input_ut |
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180 $editing_functions.replace_output_tu |
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181 $editing_functions.replace_output_ut |
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182 ### Unaligning |
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183 $editing_functions.unalign_input |
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184 $editing_functions.unalign_output |
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185 ### Removing Duplicates |
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186 $editing_functions.deduplicate_ids |
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187 #if str($editing_functions.deduplicate_ids) |
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188 --duporder '$editing_functions.duporder' |
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189 #end if |
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190 ]]></command> |
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191 <inputs> |
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192 <param name="input" type="data" format="fasta,fasta.gz" label="Input FASTA" help="Upload a multiple sequence alignment in FASTA or compressed FASTA (.gz) format."/> <!-- BASIC options --> |
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193 <section name="basic_options" title="Basic Options" expanded="yes"> |
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194 <param argument="--all" type="boolean" truevalue="--all" falsevalue="" checked="false" label="Use All Functions" help="Enable all available functions with default parameters unless overridden."/> |
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195 <param argument="--clean" type="boolean" truevalue="--clean" falsevalue="" checked="false" label="Use All Cleaning Functions" help="Use all available cleaning functions with default parameters unless overridden."/> |
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196 <param argument="--visualise" type="boolean" truevalue="--visualise" falsevalue="" checked="false" label="Use All Visualisation Functions" help="Use all available mini alignment visualisation functions with default parameters unless overridden."/> |
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197 <param argument="--interpret" type="boolean" truevalue="--interpret" falsevalue="" checked="false" label="Use All Interpretation Functions" help="Use all available interpretation functions with default parameters unless overridden."/> |
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198 <param name="log_out" type="boolean" checked="false" label="Output log file" help="Outputs the log file."/> |
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199 </section> |
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200 |
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201 <section name="cleaning_options" title="Cleaning Options" expanded="false"> |
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202 <!-- Remove divergent options --> |
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203 <conditional name="remove_divergent_cond"> |
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204 <param name="remove_divergent_param" type="select" label="Remove divergent" help="Remove sequences with identity below a specified proportion of conserved positions."> |
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205 <option value="true">Yes</option> |
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206 <option value="false" selected="true">No</option> |
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207 </param> |
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208 <when value="true"> |
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209 <param argument="--remove_divergent_minperc" type="float" value="0.65" min="0" max="1" label="Minimum Identity Proportion" help="Minimum proportion of positions that must match the most common base or amino acid for a sequence to be kept."/> |
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210 <repeat name="remove_divergent_retain_seqs" title="sequences to retain" min="0"> |
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211 <param argument="--remove_divergent_retain" type="text" value="" label="Retain Sequence by Name" help="Always keep the sequence with this exact name. (must match a seq name)"> |
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212 <validator type="empty_field"/> |
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213 </param> |
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214 </repeat> |
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215 <repeat name="remove_divergent_retain_strings" title="strings to retain" min="0"> |
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216 <param argument="--remove_divergent_retain_str" type="text" value="" label="Retain Sequences Containing Text" help="Always keep sequences whose names contain this text."> |
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217 <validator type="empty_field"/> |
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218 </param> |
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219 </repeat> |
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220 </when> |
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221 <when value="false"/> |
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222 </conditional> |
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223 |
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224 <!-- Remove Insertions options --> |
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225 <conditional name="remove_insertions_cond"> |
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226 <param name="remove_insertions_param" type="select" label="Remove Rare Insertions" help="Remove insertions not present in the majority of sequences."> |
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227 <option value="true">Yes</option> |
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228 <option value="false" selected="true">No</option> |
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229 </param> |
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230 <when value="true"> |
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231 <param argument="--insertion_min_size" type="integer" value="3" min="1" label="Minimum Insertion Size" help="Only remove insertions larger than this number of residues. Must be less than or equal to the number of columns in your alignment."/> |
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232 <param argument="--insertion_max_size" type="integer" value="200" min="1" max="10000" label="Maximum Insertion Size" help="Only remove insertions smaller than this number of residues."/> |
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233 <param argument="--insertion_min_flank" type="integer" value="5" min="0" label="Minimum Flank Size" help="Minimum number of bases required on each side of an insertion. Must be less than half the alignment length."/> |
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c0a3b4607e66
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234 <param argument="--insertion_min_perc" type="float" value="0.5" min="0" max="1" label="Minimum Presence Proportion" help="Remove insertions found in less than this proportion of sequences."/> |
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235 </when> |
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236 <when value="false"/> |
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237 </conditional> |
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238 |
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239 <!-- Crop Ends options --> |
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240 <conditional name="crop_ends_cond"> |
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241 <param name="crop_ends_param" type="select" label="Crop Sequence Ends" help="Trim ends of sequences if they are poorly aligned."> |
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242 <option value="true">Yes</option> |
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243 <option value="false" selected="true">No</option> |
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244 </param> |
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245 <when value="true"> |
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246 <param argument="--crop_ends_mingap_perc" type="float" value="0.05" min="0" max="0.6" label="Minimum Gap Change Threshold" help="Minimum proportion of sequence length (excluding gaps) used to detect significant change in gap numbers."/> |
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c0a3b4607e66
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247 <param argument="--crop_ends_redefine_perc" type="float" value="0.1" min="0" max="0.5" label="Region Proportion to Check" help="Proportion of the sequence (excluding gaps) checked at each end to redefine cropping boundaries."/> |
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c0a3b4607e66
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248 <repeat name="crop_ends_retain_seqs" title="sequences to retain" min="0"> |
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249 <param argument="--crop_ends_retain" type="text" value="" label="Retain Sequence by Name" help="Do not crop the sequence with this exact name. (must match a seq name)"> |
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c0a3b4607e66
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250 <validator type="empty_field"/> |
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251 </param> |
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252 </repeat> |
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253 <repeat name="crop_ends_retain_strings" title="strings to retain" min="0"> |
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254 <param argument="--crop_ends_retain_str" type="text" value="" label="Retain Sequences Containing Text" help="Do not crop sequences whose names contain this text. Case-sensitive."> |
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c0a3b4607e66
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255 <validator type="empty_field"/> |
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256 </param> |
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257 </repeat> |
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258 </when> |
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259 <when value="false"/> |
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260 </conditional> |
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261 |
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262 <!-- Remove Short options --> |
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263 <conditional name="remove_short_cond"> |
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264 <param name="remove_short_param" type="select" label="Remove Short Sequences" help="Remove sequences shorter than a specified length (excluding gaps)."> |
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265 <option value="true">Yes</option> |
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266 <option value="false" selected="true">No</option> |
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267 </param> |
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268 <when value="true"> |
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269 <param argument="--remove_min_length" type="integer" value="50" min="0" label="Minimum Sequence Length" help="Remove sequences shorter than this length, excluding gaps."/> |
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c0a3b4607e66
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270 <repeat name="remove_short_retain_seqs" title="sequences to retain" min="0"> |
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271 <param argument="--remove_short_retain" type="text" value="" label="Retain Sequences by Name" help="Do not remove the sequence with this exact name. (must match a seq name)"> |
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c0a3b4607e66
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272 <validator type="empty_field"/> |
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273 </param> |
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274 </repeat> |
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275 <repeat name="remove_short_retain_strings" title="strings to retain" min="0"> |
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c0a3b4607e66
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276 <param argument="--remove_short_retain_str" type="text" value="" label="Retain Sequences Containing Text" help="Do not remove sequences whose names contain this text. Case-sensitive."> |
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277 <validator type="empty_field"/> |
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278 </param> |
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279 </repeat> |
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280 </when> |
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281 <when value="false"/> |
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282 </conditional> |
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283 |
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284 <!-- Crop Divergent options --> |
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285 <conditional name="crop_divergent_cond"> |
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286 <param name="crop_divergent_param" type="select" label="Crop Divergent Sequences" help="Remove highly divergent regions to improve alignment quality by focusing on more conserved parts."> |
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287 <option value="true">Yes</option> |
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288 <option value="false" selected="true">No</option> |
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289 </param> |
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290 <when value="true"> |
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291 <param argument="--crop_divergent_min_prop_ident" type="float" value="0.5" min="0.01" max="1" label="Minimum Identity Proportion" help="Minimum proportion of sequences that must share the same residue in a column."/> |
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292 <param argument="--crop_divergent_min_prop_nongap" type="float" value="0.5" min="0.01" max="1" label="Minimum Non-Gap Proportion" help="Minimum proportion of sequences that must contain a non-gap residue in a column."/> |
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293 <param argument="--crop_divergent_buffer_size" type="integer" value="5" min="1" label="Buffer Size" help="Number of consecutive columns that must meet the identity and non-gap criteria to retain a region."/> |
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294 </when> |
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295 <when value="false"/> |
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296 </conditional> |
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297 |
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298 <!-- Retain options --> |
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299 <conditional name="retain_cond"> |
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300 <param name="retain_param" type="select" label="Retain Specific Sequences" help="Specify sequences that should not be edited or removed during row-wise functions."> |
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301 <option value="true">Yes</option> |
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302 <option value="false" selected="true">No</option> |
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303 </param> |
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304 <when value="true"> |
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305 <repeat name="retain_seqs" title="sequences to retain" min="0"> |
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306 <param argument="--retain" type="text" value="" label="Retain Sequence with this Name" help="Do not edit or remove the sequence with this exact name during row-wise functions. Can be used multiple times. (must match a seq name)"> |
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307 <validator type="empty_field"/> |
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c0a3b4607e66
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308 </param> |
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c0a3b4607e66
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309 </repeat> |
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c0a3b4607e66
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310 <repeat name="retain_strings" title="strings to retain" min="0"> |
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c0a3b4607e66
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311 <param argument="--retain_str" type="text" value="" label="Retain Sequences Containing this String" help="Do not edit or remove sequences with names containing this text. Case-sensitive."> |
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c0a3b4607e66
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312 <validator type="empty_field"/> |
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c0a3b4607e66
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313 </param> |
|
c0a3b4607e66
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314 </repeat> |
|
c0a3b4607e66
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315 </when> |
|
c0a3b4607e66
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316 <when value="false"/> |
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c0a3b4607e66
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317 </conditional> |
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c0a3b4607e66
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318 |
|
c0a3b4607e66
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319 <param argument="--keep_gaponly" type="boolean" truevalue="--keep_gaponly" falsevalue="" checked="false" label="Keep Gap-Only Columns" help=" Keep columns in the alignment that consist entirely of gaps."/> |
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c0a3b4607e66
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320 </section> |
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c0a3b4607e66
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321 |
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c0a3b4607e66
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322 <section name="visualisation_options" title="Visualisation Options" expanded="false"> |
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c0a3b4607e66
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323 <!-- Visualisation options --> |
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c0a3b4607e66
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324 <section name="basic_visualisation_options" title="Basic Visualisation Options" expanded="false"> |
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c0a3b4607e66
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325 <param argument="--plot_input" type="boolean" checked="false" falsevalue="" truevalue="--plot_input" label="Plot input alignment" help="Visualisation of the input alignment"/> |
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c0a3b4607e66
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326 <param argument="--plot_output" type="boolean" checked="false" falsevalue="" truevalue="--plot_output" label="Plot output alignment" help="Visualisation of the cleaned output alignment"/> |
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c0a3b4607e66
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327 <param argument="--plot_markup" type="boolean" checked="false" falsevalue="" truevalue="--plot_markup" label="Plot markup" help="Visualisation of the input alignment with deleted rows and columns marked"/> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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328 <param argument="--plot_consensus_identity" type="boolean" checked="false" falsevalue="" truevalue="--plot_consensus_identity" label="Plot consensus identity" help="Plot a mini alignment showing positions which are identical to or differ from the consensus."/> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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329 <param argument="--plot_consensus_similarity" type="boolean" checked="false" falsevalue="" truevalue="--plot_consensus_similarity" label="Plot consensus similarity" help="Plot a mini alignment showing positions based on their score when when compared via a substitution matrix to the consensus."/> |
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c0a3b4607e66
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330 <conditional name="output_settings_cond"> |
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c0a3b4607e66
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331 <param name="output_settings_param" type="select" label="Change output settings?" help="Change the output settings."> |
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c0a3b4607e66
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332 <option value="true">Yes</option> |
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c0a3b4607e66
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333 <option value="false" selected="true">No</option> |
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c0a3b4607e66
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334 </param> |
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c0a3b4607e66
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335 <when value="true"> |
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c0a3b4607e66
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336 <param argument="--plot_width" type="integer" value="5" min="2" max="20" label="Plot width" help="Mini alignment width in inches."/> |
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c0a3b4607e66
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337 <param argument="--plot_height" type="integer" value="3" min="2" max="15" label="Plot height" help="Mini alignment height in inches."/> |
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c0a3b4607e66
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338 <param argument="--plot_dpi" type="integer" min="72" max="1200" value="300" label="Plot DPI" help="DPI for mini alignments"/> |
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c0a3b4607e66
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339 <param argument="--plot_keep_numbers" type="boolean" checked="false" falsevalue="" truevalue="--plot_keep_numbers" label="Plot keep numbers" help="If specified, for mini alignments based on CIAlign output with smaller than 10 sequences (or if force_numbers is switched on) the rows will be labelled based on the input alignment, rather than renumbered."/> |
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c0a3b4607e66
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340 <param argument="--plot_force_numbers" type="boolean" checked="false" falsevalue="" truevalue="--plot_force_numbers" label="Plot force numbers" help="Force all rows to be numbered on the mini alignments rather than labelling e.g. every 10th row for larger plots. Will cause labels to overlap on large plots."/> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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341 <param argument="--plot_identity_palette" type="text" value="bone" label="Plot identity palette" help="Matplotlib palette name for identity mini alignments."> |
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c0a3b4607e66
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342 <validator type="regex">^[a-zA-Z_]+$</validator> |
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c0a3b4607e66
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343 </param> |
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c0a3b4607e66
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344 <param argument="--plot_identity_gap_col" type="color" value="#ffffff" label="Plot identity gap col" help="Colour for gaps in identity mini alignments."> |
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c0a3b4607e66
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345 <sanitizer invalid_char=""> |
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c0a3b4607e66
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346 <valid initial="string.ascii_letters,string.digits"> |
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c0a3b4607e66
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347 <add value="#" /> |
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c0a3b4607e66
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348 </valid> |
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c0a3b4607e66
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349 </sanitizer> |
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c0a3b4607e66
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350 </param> |
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c0a3b4607e66
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351 <param argument="--plot_similarity_palette" type="text" value="bone" label="Plot similarity palette" help="Matplotlib palette name for similarity mini alignments."> |
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c0a3b4607e66
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352 <validator type="regex">^[a-zA-Z_]+$</validator> |
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c0a3b4607e66
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353 </param> |
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c0a3b4607e66
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354 <param argument="--plot_similarity_gap_col" type="color" value="#ffffff" label="Plot similarity gap col" help="Colour for gaps in similarity mini alignments."> |
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c0a3b4607e66
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355 <sanitizer invalid_char=""> |
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c0a3b4607e66
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356 <valid initial="string.ascii_letters,string.digits"> |
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c0a3b4607e66
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357 <add value="#" /> |
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c0a3b4607e66
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358 </valid> |
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359 </sanitizer> |
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360 </param> |
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c0a3b4607e66
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361 <param argument="--plot_sub_matrix_name" type="select" label="Substitution matrix to use for similarity plots" help="BLOSUM62 for amino acid, NUC.4.4 for nucleotide"> |
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c0a3b4607e66
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362 <option value="BLOSUM62">BLOSUM62</option> |
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c0a3b4607e66
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363 <option value="NUC.4.4" selected="true">NUC.4.4</option> |
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c0a3b4607e66
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364 </param> |
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c0a3b4607e66
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365 <param argument="--palette" type="select" value="CBS" label="Colour palette" help="Colour palette. Currently implemented CBS (colour blind safe) or bright."> |
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c0a3b4607e66
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366 <option value="CBS" selected="true">CBS</option> |
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c0a3b4607e66
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367 </param> |
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c0a3b4607e66
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368 </when> |
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369 <when value="false"/> |
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c0a3b4607e66
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370 </conditional> |
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371 </section> |
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372 |
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373 <!-- Sequence Logos --> |
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374 <conditional name="sequence_logo_cond"> |
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c0a3b4607e66
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375 <param name="sequence_logo_param" type="select" label="Make sequence logo?" help="Draw a sequence logo."> |
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c0a3b4607e66
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376 <option value="true">Yes</option> |
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c0a3b4607e66
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377 <option value="false" selected="true">No</option> |
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c0a3b4607e66
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378 </param> |
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c0a3b4607e66
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379 <when value="true"> |
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c0a3b4607e66
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380 <param argument="--sequence_logo_type" type="select" label="Type of sequence logo" help="Type of sequence logo to plot"> |
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c0a3b4607e66
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381 <option value="bar">Bar</option> |
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c0a3b4607e66
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382 <option value="text" selected="true">Text</option> |
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c0a3b4607e66
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383 <option value="both">Both (Bar and Text)</option> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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384 </param> |
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c0a3b4607e66
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385 <param argument="--sequence_logo_dpi" type="integer" min="72" max="1200" value="300" label="Resolution (DPI)" help="DPI (dots per inch) for sequence logo."/> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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386 <param argument="--sequence_logo_font" type="text" value="monospace" label="Logo Font" help="Font for bases / amino acids in a text based sequence logo"> |
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c0a3b4607e66
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387 <validator type="regex">^[a-zA-Z\- ]+$</validator> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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388 </param> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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389 <param argument="--sequence_logo_nt_per_row" type="integer" value="50" label="Number of Bases/amino acids per row" help="Number of bases / amino acids to show per row in the sequence logo, where the logo is too large to show on a single line"/> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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390 <param argument="--logo_start" type="integer" optional="true" label="Logo Start" help="Start sequence logo"/> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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391 <param argument="--logo_end" type="integer" optional="true" label="Logo End" help="End sequence logo"/> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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392 </when> |
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c0a3b4607e66
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393 <when value="false"/> |
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c0a3b4607e66
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394 </conditional> |
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c0a3b4607e66
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395 |
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c0a3b4607e66
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396 <!-- Statistics Plots --> |
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c0a3b4607e66
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397 <section name="statistics_plots" title="Statistics Plots" expanded="false"> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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398 <param argument="--plot_stats_input" type="boolean" checked="false" falsevalue="" truevalue="--plot_stats_input" label="Plot stats input" help="Plot the statistics for the input MSA"/> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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399 <param argument="--plot_stats_output" type="boolean" checked="false" falsevalue="" truevalue="--plot_stats_output" label="Plot stats output" help="Plot the statistics for the output MSA"/> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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400 <section name="stats_settings" title="Statistics Plots Settings" expanded="false"> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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401 <param argument="--plot_stats_dpi" type="integer" value="300" min="72" max="1200" label="DPI" help="DPI for coverage plot"/> |
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c0a3b4607e66
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402 <param argument="--plot_stats_width" type="integer" min="2" max="20" value="5" label="Plot width" help="Width for coverage plot (inches)"/> |
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c0a3b4607e66
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403 <param argument="--plot_stats_height" type="integer" min="2" max="15" value="3" label="Plot height" help="Height for coverage plot (inches)"/> |
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c0a3b4607e66
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404 <param argument="--plot_stats_colour" type="text" value="#0000ff" label="Colour" help="Colour for coverage plot (hex code or name)"> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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405 <sanitizer invalid_char=""> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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406 <valid initial="string.ascii_letters,string.digits"> |
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c0a3b4607e66
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407 <add value="#" /> |
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c0a3b4607e66
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408 </valid> |
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c0a3b4607e66
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409 </sanitizer> |
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c0a3b4607e66
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410 </param> |
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c0a3b4607e66
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411 </section> |
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c0a3b4607e66
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412 </section> |
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c0a3b4607e66
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413 </section> |
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c0a3b4607e66
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414 |
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c0a3b4607e66
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415 |
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c0a3b4607e66
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416 <section name="interpretation_options" title="Interpretation Options" expanded="false"> |
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c0a3b4607e66
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417 <!-- Consensus Sequences --> |
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c0a3b4607e66
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418 <conditional name="consensus_sequences_cond"> |
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c0a3b4607e66
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419 <param name="consensus_sequences_param" type="select" label="Consensus Sequences" help="This generates a consensus sequence based on the cleaned alignment."> |
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c0a3b4607e66
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420 <option value="true">Yes</option> |
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c0a3b4607e66
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421 <option value="false" selected="true">No</option> |
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c0a3b4607e66
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422 </param> |
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c0a3b4607e66
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423 <when value="true"> |
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c0a3b4607e66
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424 <!-- consensus_sequences --> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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425 <param argument="--consensus_type" type="select" label="Type of consensus sequence" help="Can be majority, to use the most common character at each position in the consensus, even if this is a gap, or majority_nongap, to use the most common non-gap character at each position"> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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426 <option value="majority" selected="true">majority</option> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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427 <option value="majority_nongap">majority_nongap</option> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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428 </param> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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429 <param argument="--consensus_keep_gaps" type="boolean" truevalue="--consensus_keep_gaps" falsevalue="" checked="false" label="Include gaps?" help="Should gaps be included in the consensus"/> |
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c0a3b4607e66
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430 </when> |
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c0a3b4607e66
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431 <when value="false"/> |
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c0a3b4607e66
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432 </conditional> |
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c0a3b4607e66
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433 |
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c0a3b4607e66
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434 <!-- Position Matrices --> |
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c0a3b4607e66
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435 <section name="position_matrices" title="Position Matrices" expanded="false"> |
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c0a3b4607e66
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436 <param argument="--pwm_input" type="boolean" checked="false" falsevalue="" truevalue="--pwm_input" label="Generate input matrices" help="Generate a position frequency matrix, position probability matrix and position weight matrix based on the input alignment"/> |
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c0a3b4607e66
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437 <param argument="--pwm_output" type="boolean" checked="false" falsevalue="" truevalue="--pwm_output" label="Generate output matrices" help="Generate a position frequency matrix, position probability matrix and position weight matrix based on the cleaned output alignment"/> |
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c0a3b4607e66
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438 <section name="matrices_settings" title="Position Matrices Settings" expanded="false"> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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439 <param argument="--pwm_start" type="integer" optional="true" label="Start the PWM" help="Start the PWM and other matrices from this column of the input alignment"/> |
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c0a3b4607e66
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440 <param argument="--pwm_end" type="integer" optional="true" label="End the PWM" help="End the PWM and other matrices at this column of the input alignment"/> |
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c0a3b4607e66
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441 <param argument="--pwm_freqtype" type="select" label="Background frequency matrix" help="Choose how to compute background frequencies for the PWM: - equal: assume all residues are equally common |
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c0a3b4607e66
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442 - calc: derive from the input PFM - calc2: derive from the full alignment (same as calc if no bounds) - user: provide your own frequencies (check https://davetang.org/muse/2013/10/01/position-weight-matrix/)"> |
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c0a3b4607e66
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443 <option value="user">user</option> |
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c0a3b4607e66
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444 <option value="equal" selected="true">equal</option> |
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c0a3b4607e66
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445 <option value="calc">calc</option> |
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c0a3b4607e66
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446 <option value="calc2">calc2</option> |
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c0a3b4607e66
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447 </param> |
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c0a3b4607e66
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448 <param argument="--pwm_alphatype" type="select" label="Pseudocount type" help="If alphatype is 'calc', alpha is calculated as frequency(base), If alpha type is 'user' the user provides the value of alpha as pwm_alphatype. To run without pseudocounts set pwm_alphatype as user and pwm_alphaval as 0."> |
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c0a3b4607e66
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449 <option value="user">user</option> |
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c0a3b4607e66
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450 <option value="calc" selected="true">calc</option> |
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c0a3b4607e66
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451 </param> |
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c0a3b4607e66
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452 <param argument="--pwm_alphaval" type="integer" value="1" label="Alpha value" help="User defined value of the alpha parameter to use as a pseudocount in the PPM."/> |
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c0a3b4607e66
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453 </section> |
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c0a3b4607e66
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454 <param argument="--pwm_output_blamm" type="boolean" checked="false" falsevalue="" truevalue="--pwm_output_blamm" label="Output for BLAM" help="Output PPM formatted for BLAMM software"/> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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455 <param argument="--pwm_output_meme" type="boolean" checked="false" falsevalue="" truevalue="--pwm_output_meme" label="Output for MEME" help="Output PPM formatted for MEME software"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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parents:
diff
changeset
|
456 </section> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
457 |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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parents:
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changeset
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458 <!-- Similarity Matrices --> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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parents:
diff
changeset
|
459 <section name="similarity_matrices" title="Similarity Matrices" expanded="false"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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parents:
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changeset
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460 <param argument="--make_similarity_matrix_input" type="boolean" checked="false" falsevalue="" truevalue="--make_similarity_matrix_input" label="Input similarity matrix" help="Make a similarity matrix for the input alignment"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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parents:
diff
changeset
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461 <param argument="--make_similarity_matrix_output" type="boolean" checked="false" falsevalue="" truevalue="--make_similarity_matrix_output" label="Output similarity matrix" help="Make a similarity matrix for the output alignment"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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parents:
diff
changeset
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462 <section name="similarity_matrices_settings" title="Similarity Matrices Settings" expanded="false"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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changeset
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463 <param argument="--make_simmatrix_keepgaps" type="select" label="Keep gaps" help="0 - exclude positions which are gaps in either or both sequences from similarity calculations, 1 - exclude positions which are gaps in both sequences, 2 - include all positions"> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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changeset
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464 <option value="0" selected="true">0</option> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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changeset
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465 <option value="1">1</option> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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changeset
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466 <option value="2">2</option> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
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changeset
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467 </param> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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468 <param argument="--make_simmatrix_dp" type="integer" min="0" max="10" value="4" label="Decimal places" help="Number of decimal places to display in the similarity matrix output file"/> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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469 <param argument="--make_simmatrix_minoverlap" type="integer" value="1" label="Minimum overlap" help="Minimum overlap between two sequences to have non-zero similarity in the similarity matrix"/> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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470 </section> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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changeset
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471 </section> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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changeset
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472 </section> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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473 |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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474 <!-- Editing Functions --> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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475 <section name="editing_functions" title="Editing Options" expanded="false"> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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476 <!-- get section --> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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changeset
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477 <conditional name="get_section_cond"> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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478 <param name="get_section_param" type="select" label="Retrieve and process a section of the alignment?"> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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479 <option value="true" >Yes</option> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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480 <option value="false" selected="true">No</option> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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481 </param> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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482 <when value="true"> |
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1
3c5bdab3c7b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit 4272ec0a9c9fc6c2a54aa702a3dc446ec598ffcc
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diff
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483 <param argument="--section_start" value="" type="integer" label="Section start" help="Start position in the original alignment for the section to be extracted"/> |
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3c5bdab3c7b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit 4272ec0a9c9fc6c2a54aa702a3dc446ec598ffcc
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484 <param argument="--section_end" value="" type="integer" label="Section end" help="End position in the original alignment for the section to be extracted"/> |
|
0
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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485 </when> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
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486 <when value="false"/> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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487 </conditional> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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changeset
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488 <!-- replace bases--> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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changeset
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489 <param argument="--replace_input_tu" type="boolean" checked="false" falsevalue="" truevalue="--replace_input_tu" label="Replace input T - U " help="Generates a copy of the input alignment with U's instead of T's"/> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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changeset
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490 <param argument="--replace_input_ut" type="boolean" checked="false" falsevalue="" truevalue="--replace_input_ut" label="Replace input U - T " help="Generates a copy of the input alignment with T's instead of U's"/> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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491 <param argument="--replace_output_tu" type="boolean" checked="false" falsevalue="" truevalue="--replace_output_tu" label="Replace output T - U " help="Generates a copy of the output alignment with U's instead of T's"/> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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changeset
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492 <param argument="--replace_output_ut" type="boolean" checked="false" falsevalue="" truevalue="--replace_output_ut" label="Replace output U -T " help="Generates a copy of the output alignment with T's instead of U's"/> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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changeset
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493 <!-- Unaligning --> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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494 <param argument="--unalign_input" type="boolean" checked="false" falsevalue="" truevalue="--unalign_input" label="Input alignment with no gaps " help="Generates a copy of the input alignment with no gaps"/> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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495 <param argument="--unalign_output" type="boolean" checked="false" falsevalue="" truevalue="--unalign_output" label="Out alignment with no gaps " help="Generates a copy of the output alignment with no gaps"/> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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496 <param argument="--deduplicate_ids" type="boolean" checked="false" falsevalue="" truevalue="--deduplicate_ids" label="Remove duplicates" help="Remove sequences with duplicate names from the input."/> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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497 <param argument="--duporder" type="select" label="Duplicates order" help="Set to first to keep the first instance of the sequence name and last to keep the last"> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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498 <option value="first" selected="true">first</option> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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changeset
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499 <option value="last">last</option> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
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changeset
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500 </param> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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parents:
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changeset
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501 </section> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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502 </inputs> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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parents:
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changeset
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503 |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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504 <outputs> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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505 <data name="output_cleaned" format="fasta" from_work_dir="output_cleaned.fasta" label="${tool.name} on ${on_string}: Cleaned Alignment"/> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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506 <data name="output_removed" format="txt" from_work_dir="output_removed.txt" label="${tool.name} on ${on_string}: Removed Sequences"/> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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507 <data name="output_log" format="txt" from_work_dir="output_log.txt" label="${tool.name} on ${on_string}: Log File"> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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508 <filter>basic_options['log_out']</filter> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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changeset
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509 </data> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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510 <!-- Visualisation Options Simple Outputs --> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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511 <data name="plot_input" format="png" from_work_dir="output_input.png" label="${tool.name} on ${on_string}: Input Plot"> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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512 <filter>visualisation_options['basic_visualisation_options']['plot_input'] or basic_options['visualise'] or basic_options['all']</filter> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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513 </data> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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514 <data name="plot_output" format="png" from_work_dir="output_output.png" label="${tool.name} on ${on_string}: Output Plot"> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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changeset
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515 <filter>visualisation_options['basic_visualisation_options']['plot_output'] or basic_options['visualise'] or basic_options['all']</filter> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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changeset
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516 </data> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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517 <data name="plot_markup" format="png" from_work_dir="output_markup.png" label="${tool.name} on ${on_string}: Markup Plot"> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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changeset
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518 <filter>visualisation_options['basic_visualisation_options']['plot_markup'] or basic_options['visualise'] or basic_options['all']</filter> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
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changeset
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519 </data> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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changeset
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520 <data name="plot_markup_legend" format="png" from_work_dir="output_markup_legend.png" label="${tool.name} on ${on_string}: Markup Legend"> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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changeset
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521 <filter>visualisation_options['basic_visualisation_options']['plot_markup'] or basic_options['visualise'] or basic_options['all']</filter> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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parents:
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changeset
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522 </data> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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523 <data name="plot_consensus_identity" format="png" from_work_dir="output_consensus_identity.png" label="${tool.name} on ${on_string}: Consensus Identity Plot"> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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changeset
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524 <filter>visualisation_options['basic_visualisation_options']['plot_consensus_identity'] or basic_options['all']</filter> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
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changeset
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525 </data> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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526 <data name="plot_consensus_similarity" format="png" from_work_dir="output_consensus_similarity.png" label="${tool.name} on ${on_string}: Consensus Similarity Plot"> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
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changeset
|
527 <filter>visualisation_options['basic_visualisation_options']['plot_consensus_similarity']</filter> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
528 </data> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
529 <!-- Visualisation Options Outputs --> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
530 <data name="logo_bar" format="png" from_work_dir="output_logo_bar.png" label="${tool.name} on ${on_string}: Logo Bar Chart"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
531 <filter>(visualisation_options['sequence_logo_cond']['sequence_logo_param'] == 'true' and (visualisation_options['sequence_logo_cond']['sequence_logo_type'] == 'bar' or visualisation_options['sequence_logo_cond']['sequence_logo_type'] == 'both'))</filter> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
532 </data> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
533 <data name="logo_text" format="png" from_work_dir="output_logo_text.png" label="${tool.name} on ${on_string}: Logo Text Chart"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
534 <filter>(visualisation_options['sequence_logo_cond']['sequence_logo_param'] == 'true' and (visualisation_options['sequence_logo_cond']['sequence_logo_type'] == 'text' or visualisation_options['sequence_logo_cond']['sequence_logo_type'] == 'both'))</filter> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
535 </data> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
536 |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
537 <!-- Statistics plots of the input --> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
538 <collection name="plot_stats_input" type="list" label="Input stats plots"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
539 <discover_datasets pattern="(output_input_)(?P<designation>.+)\.png$" format="png" directory="." visible="false"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
540 <filter>visualisation_options['statistics_plots']['plot_stats_input'] or basic_options['interpret'] or basic_options['all']</filter> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
541 </collection> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
542 |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
543 <!-- Statistics plots of the output --> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
544 <collection name="plot_stats_outputs" type="list" label="Output stats plots"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
545 <discover_datasets pattern="(output_output_)(?P<designation>.+)\.png$" format="png" directory="." visible="false"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
546 <filter>visualisation_options['statistics_plots']['plot_stats_output'] or basic_options['interpret'] or basic_options['all']</filter> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
547 </collection> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
548 |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
549 <!-- Interpretaion Options Outputs --> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
550 <data name="output_consensus" format="fasta" from_work_dir="output_consensus.fasta" label="${tool.name} on ${on_string}: Consensus Sequence"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
551 <filter>interpretation_options['consensus_sequences_cond']['consensus_sequences_param'] == 'true' or basic_options['interpret'] or basic_options['all']</filter> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
552 </data> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
553 <data name="output_with_consensus" format="fasta" from_work_dir="output_with_consensus.fasta" label="${tool.name} on ${on_string}: Cleaned + Consensus"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
554 <filter>interpretation_options['consensus_sequences_cond']['consensus_sequences_param'] == 'true' or basic_options['interpret'] or basic_options['all']</filter> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
555 </data> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
556 <data name="pwm_input" format="txt" from_work_dir="output_pwm_input.txt" label="${tool.name} on ${on_string}: PWM Input"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
557 <filter>interpretation_options['position_matrices']['pwm_input']</filter> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
558 </data> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
559 <data name="ppm_input" format="txt" from_work_dir="output_ppm_input.txt" label="${tool.name} on ${on_string}: PPM Input"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
560 <filter>interpretation_options['position_matrices']['pwm_input']</filter> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
561 </data> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
562 <data name="pfm_input" format="txt" from_work_dir="output_pfm_input.txt" label="${tool.name} on ${on_string}: PFM Input"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
563 <filter>interpretation_options['position_matrices']['pwm_input']</filter> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
564 </data> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
565 <data name="ppm_meme_input" format="txt" from_work_dir="output_ppm_meme_input.txt" label="${tool.name} on ${on_string}: PPM for MEME (Input)"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
566 <filter>interpretation_options['position_matrices']['pwm_input'] and interpretation_options['position_matrices']['pwm_output_meme']</filter> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
567 </data> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
568 <data name="blamm_input" format="txt" from_work_dir="output_pfm_blamm_input.txt" label="${tool.name} on ${on_string}: PFM for BLAMM (Input)"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
569 <filter>interpretation_options['position_matrices']['pwm_input'] and interpretation_options['position_matrices']['pwm_output_blamm']</filter> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
570 </data> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
571 <data name="pwm_output" format="txt" from_work_dir="output_pwm_output.txt" label="${tool.name} on ${on_string}: PWM Output"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
572 <filter>interpretation_options['position_matrices']['pwm_output']</filter> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
573 </data> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
574 <data name="ppm_output" format="txt" from_work_dir="output_ppm_output.txt" label="${tool.name} on ${on_string}: PPM Output"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
575 <filter>interpretation_options['position_matrices']['pwm_output']</filter> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
576 </data> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
577 <data name="pfm_output" format="txt" from_work_dir="output_pfm_output.txt" label="${tool.name} on ${on_string}: PFM Output"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
578 <filter>interpretation_options['position_matrices']['pwm_output']</filter> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
579 </data> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
580 <data name="ppm_meme_output" format="txt" from_work_dir="output_ppm_meme_output.txt" label="${tool.name} on ${on_string}: PPM for MEME (Output)"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
581 <filter>interpretation_options['position_matrices']['pwm_output'] and interpretation_options['position_matrices']['pwm_output_meme']</filter> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
582 </data> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
583 <data name="blamm_output" format="txt" from_work_dir="output_pfm_blamm_output.txt" label="${tool.name} on ${on_string}: PFM for BLAMM (Output)"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
584 <filter>interpretation_options['position_matrices']['pwm_output'] and interpretation_options['position_matrices']['pwm_output_blamm']</filter> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
585 </data> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
586 <data name="input_similarity" format="tsv" from_work_dir="output_input_similarity.tsv" label="${tool.name} on ${on_string}: Input Similarity"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
587 <filter>interpretation_options['similarity_matrices']['make_similarity_matrix_input'] or basic_options['interpret'] or basic_options['all']</filter> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
588 </data> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
589 <data name="output_similarity" format="tsv" from_work_dir="output_output_similarity.tsv" label="${tool.name} on ${on_string}: Output Similarity"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
590 <filter>interpretation_options['similarity_matrices']['make_similarity_matrix_output'] or basic_options['interpret'] or basic_options['all']</filter> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
591 </data> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
592 <data name="output_output_column_stats" format="tsv" from_work_dir="output_output_column_stats.tsv" label="${tool.name} on ${on_string}: Output column stats"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
593 <filter>basic_options['interpret'] or basic_options['all']</filter> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
594 </data> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
595 <data name="output_input_column_stats" format="tsv" from_work_dir="output_output_column_stats.tsv" label="${tool.name} on ${on_string}: Input column stats"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
596 <filter>basic_options['interpret'] or basic_options['all']</filter> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
597 </data> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
598 <!-- Editing Options Outputs --> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
599 <data name="U_input" format="fasta" from_work_dir="output_U_input.fasta" label="${tool.name} on ${on_string}: Input: U instead of T"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
600 <filter>editing_functions['replace_input_tu']</filter> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
601 </data> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
602 <data name="T_input" format="fasta" from_work_dir="output_T_input.fasta" label="${tool.name} on ${on_string}: Input: T instead of U"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
603 <filter>editing_functions['replace_input_ut']</filter> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
604 </data> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
605 <data name="U_output" format="fasta" from_work_dir="output_U_output.fasta" label="${tool.name} on ${on_string}: Output: U instead of T"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
606 <filter>editing_functions['replace_output_tu']</filter> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
607 </data> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
608 <data name="T_output" format="fasta" from_work_dir="output_T_output.fasta" label="${tool.name} on ${on_string}: Output: T instead of U"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
609 <filter>editing_functions['replace_output_ut']</filter> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
610 </data> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
611 <data name="unaligned_input" format="fasta" from_work_dir="output_unaligned_input.fasta" label="${tool.name} on ${on_string}: Unaligned Input"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
612 <filter>editing_functions['unalign_input']</filter> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
613 </data> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
614 <data name="unaligned_output" format="fasta" from_work_dir="output_unaligned_output.fasta" label="${tool.name} on ${on_string}: Unaligned Output"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
615 <filter>editing_functions['unalign_output']</filter> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
616 </data> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
617 </outputs> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
618 <tests> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
619 <!-- Test 1 gzip files --> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
620 <test expect_num_outputs="3"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
621 <param name="input" value="example3.fasta.gz" ftype="fasta"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
622 <section name="basic_options"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
623 <param name="log_out" value="true"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
624 </section> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
625 <output name="output_cleaned" ftype="fasta"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
626 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
627 <has_n_lines n="4"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
628 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
629 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
630 <output name="output_removed" ftype="txt"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
631 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
632 <has_n_lines n="0"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
633 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
634 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
635 <output name="output_log"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
636 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
637 <has_text text="Command Line Args:"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
638 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
639 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
640 </test> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
641 <!-- Test 2 to check clean mode --> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
642 <test expect_num_outputs="3"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
643 <param name="input" value="example1.fasta" ftype="fasta"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
644 <section name="basic_options"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
645 <param name="clean" value="true"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
646 <param name="log_out" value="true"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
647 </section> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
648 <output name="output_cleaned" ftype="fasta"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
649 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
650 <has_n_lines n="10"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
651 <has_line_matching expression="AUUCUAUCUGGGUGACUAUUCGUUAUCUCUACUUACUAUCUUACUUACUUACUUACGCUACGUACUAGCUUACGUACUGACUU" /> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
652 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
653 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
654 <output name="output_removed" ftype="txt"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
655 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
656 <has_n_lines n="7"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
657 <has_line_matching expression="remove_gap_only\s+89,90,91" /> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
658 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
659 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
660 <output name="output_log"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
661 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
662 <has_text text="Command Line Args:"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
663 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
664 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
665 </test> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
666 <!-- Test 3 to clean amino acid --> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
667 <test expect_num_outputs="3"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
668 <param name="input" value="example2.fasta" ftype="fasta"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
669 <section name="basic_options"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
670 <param name="clean" value="true"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
671 <param name="log_out" value="true"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
672 </section> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
673 <section name="cleaning_options"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
674 <conditional name="retain_cond"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
675 <param name="retain_param" value="true"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
676 <repeat name="retain_seqs"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
677 <param name="retain" value="seq1"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
678 </repeat> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
679 </conditional> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
680 </section> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
681 <output name="output_cleaned" ftype="fasta"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
682 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
683 <has_n_lines n="2"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
684 <has_line_matching expression="MKTAIKDLGTEYKLTVAEYFR" /> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
685 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
686 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
687 <output name="output_removed" ftype="txt"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
688 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
689 <has_n_lines n="2"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
690 <has_line_matching expression="remove_gap_only\s+3,4" /> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
691 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
692 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
693 <output name="output_log"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
694 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
695 <has_text text="Amino acid alignment detected"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
696 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
697 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
698 </test> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
699 <!-- Test 4 to check visualise mode --> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
700 <test expect_num_outputs="7"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
701 <param name="input" value="example1.fasta" ftype="fasta"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
702 <section name="basic_options"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
703 <param name="visualise" value="true"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
704 <param name="log_out" value="true"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
705 </section> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
706 <output name="output_cleaned" ftype="fasta"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
707 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
708 <has_n_lines n="14"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
709 <has_line_matching expression="AGUCUAUCUGGGGUACUAUCUA------UCGCUACGUACUAGCUUACGUACUGACUUA--CGCUACGUACUAGCUUACGUACUGACUUA----"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
710 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
711 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
712 <output name="output_removed" ftype="txt"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
713 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
714 <has_n_lines n="1"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
715 <has_line_matching expression="remove_gap_only\s+89,90,91" /> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
716 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
717 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
718 <output name="output_log"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
719 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
720 <has_text text="Command Line Args:"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
721 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
722 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
723 <output name="plot_input" ftype="png"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
724 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
725 <has_size size="17k" delta="1k"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
726 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
727 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
728 <output name="plot_output" ftype="png"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
729 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
730 <has_size size="17k" delta="1k"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
731 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
732 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
733 <output name="plot_markup" ftype="png"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
734 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
735 <has_size size="18k" delta="1k"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
736 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
737 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
738 <output name="plot_markup_legend" ftype="png"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
739 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
740 <has_size size="11k" delta="1k"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
741 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
742 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
743 </test> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
744 <!-- Test 5 "remove divergent"" --> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
745 <test expect_num_outputs="2"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
746 <param name="input" value="example1.fasta" ftype="fasta"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
747 <section name="cleaning_options"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
748 <conditional name="remove_divergent_cond"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
749 <param name="remove_divergent_param" value="true"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
750 <param name="remove_divergent_minperc" value="0.9"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
751 <repeat name="remove_divergent_retain_seqs"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
752 <param name="remove_divergent_retain" value="Seq1"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
753 </repeat> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
754 <repeat name="remove_divergent_retain_seqs"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
755 <param name="remove_divergent_retain" value="Seq2"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
756 </repeat> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
757 </conditional> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
758 </section> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
759 <output name="output_cleaned" ftype="fasta"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
760 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
761 <has_n_lines n="10"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
762 <not_has_text text="Seq4"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
763 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
764 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
765 <output name="output_removed" ftype="txt"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
766 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
767 <has_n_lines n="2"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
768 <has_text text="remove_divergent"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
769 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
770 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
771 </test> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
772 <!-- Test 6 "remove rare insertion"" --> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
773 <test expect_num_outputs="2"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
774 <param name="input" value="example1.fasta" ftype="fasta"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
775 <section name="cleaning_options"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
776 <conditional name="remove_insertions_cond"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
777 <param name="remove_insertions_param" value="true"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
778 <param name="insertion_min_size" value="3"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
779 <param name="insertion_max_size" value="150"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
780 <param name="insertion_min_flank" value="5"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
781 <param name="insertion_min_perc" value="0.6"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
782 </conditional> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
783 </section> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
784 <output name="output_cleaned" ftype="fasta"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
785 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
786 <has_n_lines n="14"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
787 <has_line_matching expression="AGUCUAUCUGGGGUACUAUCUAUCGCUACGUACUAGCUUACGUACUGACUUA--CGCUACGUACUAGCUUACGUACUGACUUA----"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
788 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
789 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
790 <output name="output_removed" ftype="txt"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
791 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
792 <has_n_lines n="2"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
793 <has_line_matching expression="remove_gap_only\s+89,90,91"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
794 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
795 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
796 </test> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
797 <!-- Test 7 "Crop Sequence Ends"" --> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
798 <test expect_num_outputs="2"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
799 <param name="input" value="example1.fasta" ftype="fasta"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
800 <section name="cleaning_options"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
801 <conditional name="crop_ends_cond"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
802 <param name="crop_ends_param" value="true"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
803 <param name="crop_ends_mingap_perc" value="0.05"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
804 <param name="crop_ends_redefine_perc" value="0.1"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
805 <repeat name="crop_ends_retain_strings"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
806 <param name="crop_ends_retain_str" value="q7"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
807 </repeat> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
808 </conditional> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
809 </section> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
810 <output name="output_cleaned" ftype="fasta"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
811 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
812 <has_n_lines n="14"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
813 <has_line_matching expression="AUUCUAUCUGGGUACUAUUGGG------UUAUCUCUACUUACUAUCUUACAGACUUGGUUA----------------------------AAAA"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
814 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
815 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
816 <output name="output_removed" ftype="txt"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
817 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
818 <has_n_lines n="2"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
819 <has_line_matching expression="remove_gap_only\s+89,90,91"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
820 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
821 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
822 </test> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
823 <!-- Test 8 "Remove Short Sequences"" --> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
824 <test expect_num_outputs="2"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
825 <param name="input" value="example1.fasta" ftype="fasta"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
826 <section name="cleaning_options"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
827 <conditional name="remove_short_cond"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
828 <param name="remove_short_param" value="true"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
829 <param name="remove_min_length" value="70"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
830 <repeat name="remove_short_retain_seqs"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
831 <param name="remove_short_retain" value="Seq1"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
832 </repeat> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
833 <repeat name="remove_short_retain_strings"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
834 <param name="remove_short_retain_str" value="q2"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
835 </repeat> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
836 </conditional> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
837 </section> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
838 <output name="output_cleaned" ftype="fasta"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
839 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
840 <has_n_lines n="8"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
841 <not_has_text text="Seq5"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
842 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
843 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
844 <output name="output_removed" ftype="txt"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
845 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
846 <has_n_lines n="2"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
847 <has_text text="remove_too_short"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
848 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
849 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
850 </test> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
851 <!-- Test 9 "Crop Divergent" --> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
852 <test expect_num_outputs="2"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
853 <param name="input" value="example1.fasta" ftype="fasta"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
854 <section name="cleaning_options"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
855 <conditional name="crop_divergent_cond"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
856 <param name="crop_divergent_param" value="true"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
857 <param name="crop_divergent_min_prop_ident" value="0.5"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
858 <param name="crop_divergent_min_prop_nongap" value="0.5"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
859 <param name="crop_divergent_buffer_size" value="5"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
860 </conditional> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
861 </section> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
862 <output name="output_cleaned" ftype="fasta"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
863 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
864 <has_n_lines n="14"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
865 <has_line_matching expression="AUUCUAUC------UAUUGG--------UUAUCU-------------------------------------------------------"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
866 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
867 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
868 <output name="output_removed" ftype="txt"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
869 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
870 <has_n_lines n="1"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
871 <has_line_matching expression="crop_divergent\s+89,90,91,92,93,94,95"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
872 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
873 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
874 </test> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
875 <!-- Test 10 "Retain" --> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
876 <test expect_num_outputs="2"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
877 <param name="input" value="example1.fasta" ftype="fasta"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
878 <section name="cleaning_options"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
879 <conditional name="remove_short_cond"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
880 <param name="remove_short_param" value="true"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
881 <param name="remove_min_length" value="90"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
882 </conditional> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
883 <conditional name="retain_cond"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
884 <param name="retain_param" value="true"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
885 <repeat name="retain_seqs"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
886 <param name="retain" value="Seq1"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
887 </repeat> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
888 <repeat name="retain_strings"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
889 <param name="retain_str" value="q2"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
890 </repeat> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
891 </conditional> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
892 <param name="keep_gaponly" value="true"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
893 </section> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
894 <output name="output_cleaned" ftype="fasta"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
895 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
896 <has_n_lines n="4"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
897 <not_has_text text="Seq3"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
898 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
899 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
900 <output name="output_removed" ftype="txt"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
901 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
902 <has_n_lines n="1"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
903 <has_text text="remove_too_short"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
904 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
905 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
906 </test> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
907 <!-- Test 11 "Visualise basic options + settings" --> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
908 <test expect_num_outputs="6"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
909 <param name="input" value="example1.fasta" ftype="fasta"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
910 <section name="visualisation_options"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
911 <section name="basic_visualisation_options"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
912 <param name="plot_consensus_identity" value="true"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
913 <param name="plot_consensus_similarity" value="true"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
914 <param name="plot_markup" value="true"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
915 <conditional name="output_settings_cond"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
916 <param name="output_settings_param" value="true"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
917 <param name="plot_width" value="5"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
918 <param name="plot_height" value="3"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
919 <param name="plot_dpi" value="300"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
920 <param name="plot_keep_numbers" value="true"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
921 <param name="plot_force_numbers" value="false"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
922 <param name="plot_identity_palette" value="bone"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
923 <param name="plot_identity_gap_col" value="#ffffff"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
924 <param name="plot_similarity_palette" value="bone"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
925 <param name="plot_similarity_gap_col" value="#ffffff"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
926 <param name="palette" value="CBS"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
927 </conditional> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
928 </section> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
929 </section> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
930 <output name="output_cleaned" ftype="fasta"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
931 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
932 <has_n_lines n="14"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
933 <has_line_matching expression=">Seq1"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
934 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
935 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
936 <output name="output_removed" ftype="txt"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
937 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
938 <has_n_lines n="1"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
939 <has_line_matching expression="remove_gap_only\s+89,90,91"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
940 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
941 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
942 <output name="plot_consensus_identity" ftype="png"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
943 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
944 <has_size size="14k" delta="1k"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
945 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
946 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
947 <output name="plot_consensus_similarity" ftype="png"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
948 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
949 <has_size size="14k" delta="1k"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
950 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
951 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
952 <output name="plot_markup" ftype="png"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
953 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
954 <has_size size="17k" delta="2k"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
955 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
956 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
957 <output name="plot_markup_legend" ftype="png"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
958 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
959 <has_size size="11k" delta="1k"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
960 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
961 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
962 </test> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
963 <!-- Test 14 "Visualise statistics plots and settings" --> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
964 <test expect_num_outputs="3"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
965 <param name="input" value="example1.fasta" ftype="fasta"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
966 <section name="visualisation_options"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
967 <section name="statistics_plots"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
968 <param name="plot_stats_input" value="true"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
969 <section name="stats_settings"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
970 <param name="plot_stats_dpi" value="300"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
971 <param name="plot_stats_width" value="5"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
972 <param name="plot_stats_height" value="3"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
973 </section> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
974 </section> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
975 </section> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
976 <output name="output_cleaned" ftype="fasta"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
977 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
978 <has_n_lines n="14"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
979 <has_line_matching expression=">Seq1"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
980 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
981 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
982 <output name="output_removed" ftype="txt"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
983 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
984 <has_n_lines n="1"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
985 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
986 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
987 <output_collection name="plot_stats_input" type="list" count="5"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
988 <element name="changefreq" ftype="png"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
989 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
990 <has_size size="61k" delta="3k"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
991 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
992 </element> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
993 <element name="coverage" ftype="png"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
994 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
995 <has_size size="63k" delta="3k"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
996 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
997 </element> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
998 <element name="information_content" ftype="png"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
999 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1000 <has_size size="89k" delta="3k"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1001 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1002 </element> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1003 <element name="shannon_entropy" ftype="png"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1004 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1005 <has_size size="91k" delta="3k"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1006 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1007 </element> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1008 <element name="resfreq" ftype="png"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1009 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1010 <has_size size="77k" delta="3k"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1011 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1012 </element> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1013 </output_collection> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1014 </test> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1015 <!-- Test 15 "Consensus Sequences" --> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1016 <test expect_num_outputs="4"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1017 <param name="input" value="example1.fasta" ftype="fasta"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1018 <section name="interpretation_options"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1019 <conditional name="consensus_sequences_cond"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1020 <param name="consensus_sequences_param" value="true"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1021 <param name="consensus_type" value="majority"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1022 <param name="consensus_keep_gaps" value="true"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1023 </conditional> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1024 </section> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1025 <output name="output_cleaned" ftype="fasta"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1026 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1027 <has_n_lines n="14"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1028 <has_line_matching expression=">Seq1"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1029 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1030 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1031 <output name="output_removed" ftype="txt"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1032 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1033 <has_n_lines n="1"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1034 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1035 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1036 <output name="output_consensus" ftype="fasta"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1037 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1038 <has_n_lines n="2"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1039 <has_line_matching expression=">consensus"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1040 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1041 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1042 <output name="output_with_consensus" ftype="fasta"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1043 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1044 <has_n_lines n="16"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1045 <has_line_matching expression=">consensus"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1046 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1047 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1048 </test> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1049 <!-- Test 16 "Position Matrices" --> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1050 <test expect_num_outputs="7"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1051 <param name="input" value="example1.fasta" ftype="fasta"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1052 <section name="interpretation_options"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1053 <section name="position_matrices"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1054 <param name="pwm_input" value="true"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1055 <section name="matrices_settings"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1056 <param name="pwm_start" value="1"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1057 <param name="pwm_end" value="100"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1058 <param name="pwm_freqtype" value="equal"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1059 <param name="pwm_alphatype" value="calc"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1060 <param name="pwm_alphaval" value="1"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1061 </section> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1062 <param name="pwm_output_blamm" value="true"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1063 <param name="pwm_output_meme" value="true"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1064 </section> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1065 </section> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1066 <output name="output_cleaned" ftype="fasta"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1067 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1068 <has_n_lines n="14"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1069 <has_line_matching expression=">Seq1"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1070 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1071 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1072 <output name="output_removed" ftype="txt"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1073 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1074 <has_n_lines n="1"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1075 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1076 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1077 <output name="pwm_input" ftype="txt"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1078 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1079 <has_n_lines n="5"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1080 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1081 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1082 <output name="ppm_input" ftype="txt"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1083 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1084 <has_n_lines n="5"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1085 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1086 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1087 <output name="pfm_input" ftype="txt"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1088 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1089 <has_n_lines n="5"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1090 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1091 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1092 <output name="ppm_meme_input" ftype="txt"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1093 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1094 <has_n_lines n="103"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1095 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1096 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1097 <output name="blamm_input" ftype="txt"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1098 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1099 <has_n_lines n="5"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1100 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1101 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1102 </test> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1103 <!-- Test 17 "Similarity Sequences" --> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1104 <test expect_num_outputs="3"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1105 <param name="input" value="example1.fasta" ftype="fasta"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1106 <section name="interpretation_options"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1107 <section name="similarity_matrices"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1108 <param name="make_similarity_matrix_input" value="true"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1109 <section name="similarity_matrices_settings"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1110 <param name="make_simmatrix_keepgaps" value="0"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1111 <param name="make_simmatrix_dp" value="4"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1112 <param name="make_simmatrix_minoverlap" value="1"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1113 </section> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1114 </section> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1115 </section> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1116 <output name="output_cleaned" ftype="fasta"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1117 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1118 <has_n_lines n="14"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1119 <has_line_matching expression=">Seq1"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1120 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1121 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1122 <output name="output_removed" ftype="txt"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1123 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1124 <has_n_lines n="1"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1125 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1126 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1127 <output name="input_similarity" ftype="tsv"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1128 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1129 <has_n_lines n="8"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1130 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1131 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1132 </test> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1133 <!-- Test 18 "Extract Part of Alignment" --> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1134 <test expect_num_outputs="2"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1135 <param name="input" value="example1.fasta" ftype="fasta"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1136 <section name="editing_functions"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1137 <conditional name="get_section_cond"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1138 <param name="get_section_param" value="true"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1139 <param name="section_start" value="10"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1140 <param name="section_end" value="50"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1141 </conditional> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1142 </section> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1143 <output name="output_cleaned" ftype="fasta"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1144 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1145 <has_n_lines n="14"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1146 <has_line_matching expression=">Seq1"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1147 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1148 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1149 <output name="output_removed" ftype="txt"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1150 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1151 <has_n_lines n="1"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1152 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1153 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1154 </test> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1155 <!-- Test 19 "Replace U ↔ T" --> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1156 <test expect_num_outputs="3"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1157 <param name="input" value="example1.fasta" ftype="fasta"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1158 <section name="editing_functions"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1159 <param name="replace_input_ut" value="true"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1160 </section> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1161 <output name="output_cleaned" ftype="fasta"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1162 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1163 <has_n_lines n="14"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1164 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1165 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1166 <output name="output_removed" ftype="txt"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1167 <assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1168 <has_n_lines n="1"/> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1169 </assert_contents> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1170 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1171 <output name="T_input" ftype="fasta"> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1172 <assert_contents> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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1173 <not_has_text text="U"/> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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1174 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1175 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
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1176 </test> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1177 <!-- Test 20 "Unalign (remove gaps)" --> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
diff
changeset
|
1178 <test expect_num_outputs="3"> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
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changeset
|
1179 <param name="input" value="example1.fasta" ftype="fasta"/> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
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changeset
|
1180 <section name="editing_functions"> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
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changeset
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1181 <param name="unalign_input" value="true"/> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
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changeset
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1182 </section> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
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changeset
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1183 <output name="output_cleaned" ftype="fasta"> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
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changeset
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1184 <assert_contents> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
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changeset
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1185 <has_n_lines n="14"/> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
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changeset
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1186 <has_line_matching expression=">Seq1"/> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
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changeset
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1187 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
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changeset
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1188 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
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changeset
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1189 <output name="output_removed" ftype="txt"> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
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changeset
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1190 <assert_contents> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
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changeset
|
1191 <has_n_lines n="1"/> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
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changeset
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1192 </assert_contents> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
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changeset
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1193 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
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changeset
|
1194 <output name="unaligned_input" ftype="fasta"> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
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changeset
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1195 <assert_contents> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
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changeset
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1196 <not_has_text text="-"/> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
parents:
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changeset
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1197 </assert_contents> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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changeset
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1198 </output> |
|
c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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parents:
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changeset
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1199 </test> |
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c0a3b4607e66
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changeset
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1200 <!-- Test 21 "Remove Duplicates" --> |
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c0a3b4607e66
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changeset
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1201 <test expect_num_outputs="2"> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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changeset
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1202 <param name="input" value="example1.fasta" ftype="fasta"/> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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changeset
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1203 <section name="editing_functions"> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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1204 <param name="deduplicate_ids" value="true"/> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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changeset
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1205 </section> |
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c0a3b4607e66
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1206 <output name="output_cleaned" ftype="fasta"> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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changeset
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1207 <assert_contents> |
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c0a3b4607e66
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changeset
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1208 <has_n_lines n="14"/> |
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c0a3b4607e66
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changeset
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1209 <has_line_matching expression=">Seq1"/> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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changeset
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1210 </assert_contents> |
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c0a3b4607e66
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1211 </output> |
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c0a3b4607e66
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1212 <output name="output_removed" ftype="txt"> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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changeset
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1213 <assert_contents> |
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c0a3b4607e66
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changeset
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1214 <has_n_lines n="1"/> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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changeset
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1215 </assert_contents> |
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c0a3b4607e66
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1216 </output> |
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c0a3b4607e66
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changeset
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1217 </test> |
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c0a3b4607e66
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1218 </tests> |
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c0a3b4607e66
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parents:
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changeset
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1219 <expand macro="help"/> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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changeset
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1220 <citations> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
iuc
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1221 <citation type="doi">10.7717/peerj.12983</citation> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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1222 </citations> |
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c0a3b4607e66
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parents:
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changeset
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1223 <expand macro="creator"/> |
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c0a3b4607e66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit fab1845778b34ff4166b2aa3efd4c88d240adb24
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1224 </tool> |