Mercurial > repos > iuc > teloscope
annotate teloscope.xml @ 1:089c6e8122c8 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 04870df78442ec883c2d8463d5958c94317a7d8d
| author | iuc |
|---|---|
| date | Wed, 03 Dec 2025 18:54:06 +0000 |
| parents | be2c72b9798b |
| children |
| rev | line source |
|---|---|
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
diff
changeset
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1 <tool id="teloscope" name="Teloscope" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
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changeset
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2 <description>Assembly telomere annotation</description> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
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changeset
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3 <macros> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
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4 <import>macros.xml</import> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
diff
changeset
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5 </macros> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
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changeset
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6 <expand macro="requirements"/> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
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changeset
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7 <version_command>teloscope -v</version_command> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
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8 <command detect_errors="exit_code"><![CDATA[ |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
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9 mkdir -p output && |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
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changeset
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10 teloscope |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
diff
changeset
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11 --input-sequence '$input_sequence' |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
diff
changeset
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12 --output output |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
diff
changeset
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13 --canonical '$canonical' |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
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changeset
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14 --patterns '$patterns' |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
diff
changeset
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15 --window '$window' |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
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16 --step '$step' |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
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17 --threads "\${GALAXY_SLOTS:-2}" |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
diff
changeset
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18 --terminal-limit '$terminal_limit' |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
diff
changeset
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19 --max-match-distance '$max_match_distance' |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
diff
changeset
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20 --max-block-distance '$max_block_distance' |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
diff
changeset
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21 --min-block-length '$min_block_length' |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
diff
changeset
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22 --min-block-density '$min_block_density' |
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1
089c6e8122c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 04870df78442ec883c2d8463d5958c94317a7d8d
iuc
parents:
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23 --edit-distance '$edit_distance' |
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0
be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
diff
changeset
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24 |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
diff
changeset
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25 $out_win_repeats |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
diff
changeset
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26 $out_gc |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
diff
changeset
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27 $out_entropy |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
diff
changeset
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28 $out_matches |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
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changeset
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29 $out_its |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
diff
changeset
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30 $ultra_fast |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
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changeset
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31 $verbose |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
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32 > output/${input_sequence.name}.telo.report |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
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33 ]]></command> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
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changeset
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34 <inputs> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
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changeset
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35 <param argument="--input-sequence" type="data" format="fasta,fasta.gz" label="Input assembly"/> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
diff
changeset
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36 <param argument="--canonical" type="text" value="TTAGGG" label="Canonical telomeric pattern"> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
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changeset
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37 <sanitizer> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
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changeset
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38 <valid initial="string.printable"> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
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39 <remove value=" "/> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
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40 <remove value="\t"/> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
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41 <remove value="\r"/> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
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42 <remove value="\n"/> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
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43 </valid> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
diff
changeset
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44 </sanitizer> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
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45 <validator type="regex" message="Canonical must contain only A,C,G,T.">^[ACGTacgt]+$</validator> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
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46 </param> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
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47 |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
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48 <param argument="--patterns" type="text" value="TTAGGG,CCCTAA" |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
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49 label="Patterns to explore (comma-separated), IUPAC allowed"> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
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50 <validator type="regex" |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
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51 message="Use IUPAC letters ACGTRYSWKMBDHVN; comma-separated.">^[ACGTRYSWKMBDHVNacgtryswkmbdhvn]+(?:,[ACGTRYSWKMBDHVNacgtryswkmbdhvn]+)*$</validator> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
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changeset
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52 </param> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
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53 |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
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54 <param argument="--window" type="integer" min="100" value="1000" label="Sliding window size"/> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
diff
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55 <param argument="--step" type="integer" min="100" value="500" label="Sliding window step"/> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
diff
changeset
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56 <param argument="--terminal-limit" type="integer" min="10000" value="50000" label="Terminal limit (bp) in contigs"/> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
diff
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57 <param argument="--max-match-distance" type="integer" min="0" value="50" label="Maximum distance (bp) for merging matches"/> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
diff
changeset
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58 <param argument="--max-block-distance" type="integer" min="0" value="200" label="Maximum block distance for merging"/> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
diff
changeset
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59 <param argument="--min-block-length" type="integer" min="0" value="500" label="Minimum block length"/> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
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60 <param argument="--min-block-density" type="float" min="0" max="1" value="0.5" label="Minimum block density (0–1)"/> |
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1
089c6e8122c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 04870df78442ec883c2d8463d5958c94317a7d8d
iuc
parents:
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61 <param argument="--edit-distance" type="integer" min="0" max="2" value="0" label="Edit distance for pattern matching (0–2)"/> |
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0
be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
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62 |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
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63 <param argument="--out-win-repeats" type="boolean" truevalue="--out-win-repeats" falsevalue="" checked="false" label="Window repeat counts"/> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
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64 <param argument="--out-gc" type="boolean" truevalue="--out-gc" falsevalue="" checked="false" label="Window GC"/> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
diff
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65 <param argument="--out-entropy" type="boolean" truevalue="--out-entropy" falsevalue="" checked="false" label="Window Shannon entropy"/> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
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66 <param argument="--out-matches" type="boolean" truevalue="--out-matches" falsevalue="" checked="false" label="Canonical/NonCanonical Matches"/> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
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67 <param argument="--out-its" type="boolean" truevalue="--out-its" falsevalue="" checked="false" label="Interstitial telomeres (ITSs)"/> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
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68 <param argument="--ultra-fast" type="boolean" truevalue="--ultra-fast" falsevalue="" checked="true" label="Ultra-fast mode (terminal regions only)"/> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
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69 <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="false" label="Verbose output"/> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
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70 </inputs> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
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71 |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
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72 <outputs> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
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73 <!-- BASIC OUTFILES --> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
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74 <data name="terminal_telomeres" format="bed" from_work_dir="output/*_terminal_telomeres.bed" label="${tool.name} on ${on_string}: Terminal telomeres"/> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
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75 <data name="telo_report" format="tabular" from_work_dir="output/*.telo.report" label="${tool.name} on ${on_string}: Summary report"/> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
parents:
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76 |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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changeset
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77 <!-- OPTIONAL OUTFILES --> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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78 <data name="interstitial_telomeres" format="bed" from_work_dir="output/*_interstitial_telomeres.bed" label="${tool.name} on ${on_string}: Interstitial telomeres"> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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79 <filter>out_its</filter> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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parents:
diff
changeset
|
80 </data> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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81 <data name="canonical_matches" format="bed" from_work_dir="output/*_canonical_matches.bed" label="${tool.name} on ${on_string}: Canonical matches"> |
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be2c72b9798b
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82 <filter>out_matches</filter> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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parents:
diff
changeset
|
83 </data> |
|
be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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84 <data name="noncanonical_matches" format="bed" from_work_dir="output/*_noncanonical_matches.bed" label="${tool.name} on ${on_string}: Noncanonical matches"> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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changeset
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85 <filter>out_matches</filter> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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diff
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|
86 </data> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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87 <data name="window_metrics" format="bedgraph" from_work_dir="output/*_window_metrics.bedgraph" label="${tool.name} on ${on_string}: Window metrics"> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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88 <filter>out_gc or out_entropy or out_win_repeats</filter> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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89 </data> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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90 </outputs> |
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be2c72b9798b
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changeset
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91 |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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92 <tests> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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93 <!-- 1) Default (-u) : terminal telomeres + report --> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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94 <test expect_num_outputs="2"> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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95 <param name="input_sequence" value="bTaeGut7_chr33_mat.fa.gz" ftype="fasta.gz"/> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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96 <param name="canonical" value="TTAGGG"/> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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97 <param name="patterns" value="TTAGGG,CCCTAA"/> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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98 <output name="terminal_telomeres"> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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99 <assert_contents> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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100 <!-- at least one BED-like line (match whole line to allow extra cols) --> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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101 <has_line_matching expression="^\S+\t\d+\t\d+(?:\t.*)?$"/> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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102 </assert_contents> |
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be2c72b9798b
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103 </output> |
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be2c72b9798b
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104 <output name="telo_report"> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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105 <assert_contents> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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106 <has_line_matching expression="\+\+\+ Path Summary Report \+\+\+"/> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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107 <has_line_matching expression="\+\+\+ Assembly Summary Report \+\+\+"/> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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108 <has_line_matching expression="\+\+\+ Telomere Statistics \+\+\+"/> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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109 <has_line_matching expression="\+\+\+ Chromosome Telomere Counts\+\+\+"/> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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110 <has_line_matching expression="\+\+\+ Chromosome Telomere/Gap Completeness\+\+\+"/> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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111 </assert_contents> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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112 </output> |
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be2c72b9798b
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113 </test> |
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114 |
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be2c72b9798b
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115 <!-- 2) Genome-wide (-g -e -r -m -i ; disable -u) --> |
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be2c72b9798b
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116 <test expect_num_outputs="6"> |
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117 <param name="input_sequence" value="bTaeGut7_chr33_mat.fa.gz" ftype="fasta.gz"/> |
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be2c72b9798b
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118 <param name="canonical" value="TTAGGG"/> |
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be2c72b9798b
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119 <param name="patterns" value="TTAGGG,CCCTAA"/> |
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be2c72b9798b
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120 <param name="out_gc" value="true"/> |
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be2c72b9798b
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121 <param name="out_entropy" value="true"/> |
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be2c72b9798b
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122 <param name="out_win_repeats" value="true"/> |
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be2c72b9798b
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123 <param name="out_matches" value="true"/> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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124 <param name="out_its" value="true"/> |
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be2c72b9798b
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125 <param name="ultra_fast" value="false"/> |
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126 |
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127 <output name="terminal_telomeres"> |
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128 <assert_contents> |
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129 <has_line_matching expression="^\S+\t\d+\t\d+(?:\t.*)?$"/> |
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130 </assert_contents> |
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131 </output> |
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132 <output name="interstitial_telomeres"> |
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133 <assert_contents> |
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134 <has_line_matching expression="^\S+\t\d+\t\d+(?:\t.*)?$"/> |
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135 </assert_contents> |
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136 </output> |
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137 <output name="canonical_matches"> |
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138 <assert_contents> |
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139 <!-- ensure at least one CCCTAA match line --> |
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140 <has_line_matching expression="^\S+\t\d+\t\d+\tCCCTAA(?:\s|$)"/> |
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141 </assert_contents> |
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142 </output> |
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143 <output name="noncanonical_matches"> |
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144 <assert_contents> |
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145 <!-- expect an empty file --> |
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146 <has_n_lines n="0"/> |
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147 </assert_contents> |
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148 </output> |
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149 <output name="window_metrics"> |
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150 <assert_contents> |
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151 <has_text text="track type=bedGraph"/> |
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152 <!-- first data window line --> |
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be2c72b9798b
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153 <has_line_matching expression="^\S+\t0\t1000\t.*"/> |
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154 </assert_contents> |
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155 </output> |
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156 <output name="telo_report"> |
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157 <assert_contents> |
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158 <has_line_matching expression="\+\+\+ Path Summary Report \+\+\+"/> |
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159 <has_line_matching expression="\+\+\+ Assembly Summary Report \+\+\+"/> |
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160 <has_line_matching expression="\+\+\+ Telomere Statistics \+\+\+"/> |
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161 <has_line_matching expression="\+\+\+ Chromosome Telomere Counts\+\+\+"/> |
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162 <has_line_matching expression="\+\+\+ Chromosome Telomere/Gap Completeness\+\+\+"/> |
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163 </assert_contents> |
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164 </output> |
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165 </test> |
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166 |
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167 <!-- 3) Edit distance 1: more variants detected --> |
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168 <test expect_num_outputs="2"> |
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169 <param name="input_sequence" value="bTaeGut7_chr33_mat.fa.gz" ftype="fasta.gz"/> |
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170 <param name="canonical" value="TTAGGG"/> |
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171 <param name="patterns" value="TTAGGG,CCCTAA"/> |
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172 <param name="edit_distance" value="1"/> |
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173 <output name="terminal_telomeres"> |
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174 <assert_contents> |
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175 <!-- p-arm telomere with extended start due to edit distance --> |
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176 <has_text text="chr33_mat	442	14354	13912	p	"/> |
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177 <!-- q-arm telomere --> |
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178 <has_text text="chr33_mat	4219967	4246337	26370	q	"/> |
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179 </assert_contents> |
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180 </output> |
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181 <output name="telo_report"> |
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182 <assert_contents> |
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183 <has_line_matching expression="\+\+\+ Path Summary Report \+\+\+"/> |
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184 </assert_contents> |
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185 </output> |
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186 </test> |
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187 |
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188 <!-- 4) Edit distance 2: maximum variants detected --> |
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189 <test expect_num_outputs="2"> |
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190 <param name="input_sequence" value="bTaeGut7_chr33_mat.fa.gz" ftype="fasta.gz"/> |
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191 <param name="canonical" value="TTAGGG"/> |
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192 <param name="patterns" value="TTAGGG,CCCTAA"/> |
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193 <param name="edit_distance" value="2"/> |
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194 <output name="terminal_telomeres"> |
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195 <assert_contents> |
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196 <!-- p-arm telomere extends to position 1 with edit distance 2 --> |
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197 <has_text text="chr33_mat	1	14354	14353	p	"/> |
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198 <!-- q-arm telomere --> |
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199 <has_text text="chr33_mat	4219967	4246337	26370	q	"/> |
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200 </assert_contents> |
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201 </output> |
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202 <output name="telo_report"> |
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203 <assert_contents> |
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204 <has_line_matching expression="\+\+\+ Path Summary Report \+\+\+"/> |
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205 </assert_contents> |
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206 </output> |
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207 </test> |
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208 </tests> |
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209 |
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210 <help><![CDATA[ |
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211 Description: |
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212 Teloscope is a tool for telomere annotation in genome assemblies. |
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213 It scans for user-specified telomeric repeat patterns across assembly paths, contigs and windows. |
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214 Teloscope annotates terminal and interstitial telomeres, canonical/noncanonical matches and genome-wide metrics such as GC content, Shannon entropy, and repeat counts. |
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215 It generates a detailed telomere summary report for paths, telomere statistics, and chromosome labels to assess telomere completeness. |
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216 Teloscope can be used for both complete and fragmented assemblies, providing valuable information for genome manual curation and analysis. |
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217 |
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218 Usage: |
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219 Default (ultra-fast) scans terminal regions and reports terminal telomeres + a summary report. |
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220 * ${input_sequence.name}_terminal_telomeres.bed |
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221 * ${input_sequence.name}.telo.report |
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222 |
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223 Enabling window/match options (-g -e -r -m -i) performs a genome-wide scan and produces: |
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224 * ${input_sequence.name}_terminal_telomeres.bed |
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225 * ${input_sequence.name}_interstitial_telomeres.bed |
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226 * ${input_sequence.name}_canonical_matches.bed |
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227 * ${input_sequence.name}_noncanonical_matches.bed |
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228 * ${input_sequence.name}_window_metrics.bedgraph |
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229 * ${input_sequence.name}.telo.report |
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230 |
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231 Key parameters: |
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232 - -c / --canonical: Canonical repeat (default TTAGGG). This is the vertebrate telomeric motif found at chromosome ends that binds to shelterin complex to form a telomere. |
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233 - -p / --patterns: Variant patterns (comma-separated). These are additional telomeric repeat motifs to search for, besides the canonical repeat, it includes other variants that can be part of telomeres. |
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234 - -w / -s: window size / step (defaults 1000/500). |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
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235 - -u / --ultra-fast: terminal scan only (default true); disabled automatically when -g/-e/-r/-m/-i are used. |
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089c6e8122c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 04870df78442ec883c2d8463d5958c94317a7d8d
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236 - -x / --edit-distance: Edit Hamming distance for pattern matching (0–2). Useful for identifying degenerate telomeric repeats (default 0). |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
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237 ]]></help> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
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changeset
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238 |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
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239 <expand macro="citations"/> |
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be2c72b9798b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope commit 91ae0a450a15bf0a37c017b57831d40e2cea8dbc
iuc
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240 </tool> |