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comparison teloscope.xml @ 1:089c6e8122c8 draft default tip

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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
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0:be2c72b9798b 1:089c6e8122c8
18 --terminal-limit '$terminal_limit' 18 --terminal-limit '$terminal_limit'
19 --max-match-distance '$max_match_distance' 19 --max-match-distance '$max_match_distance'
20 --max-block-distance '$max_block_distance' 20 --max-block-distance '$max_block_distance'
21 --min-block-length '$min_block_length' 21 --min-block-length '$min_block_length'
22 --min-block-density '$min_block_density' 22 --min-block-density '$min_block_density'
23 --edit-distance '$edit_distance'
23 24
24 $out_win_repeats 25 $out_win_repeats
25 $out_gc 26 $out_gc
26 $out_entropy 27 $out_entropy
27 $out_matches 28 $out_matches
55 <param argument="--terminal-limit" type="integer" min="10000" value="50000" label="Terminal limit (bp) in contigs"/> 56 <param argument="--terminal-limit" type="integer" min="10000" value="50000" label="Terminal limit (bp) in contigs"/>
56 <param argument="--max-match-distance" type="integer" min="0" value="50" label="Maximum distance (bp) for merging matches"/> 57 <param argument="--max-match-distance" type="integer" min="0" value="50" label="Maximum distance (bp) for merging matches"/>
57 <param argument="--max-block-distance" type="integer" min="0" value="200" label="Maximum block distance for merging"/> 58 <param argument="--max-block-distance" type="integer" min="0" value="200" label="Maximum block distance for merging"/>
58 <param argument="--min-block-length" type="integer" min="0" value="500" label="Minimum block length"/> 59 <param argument="--min-block-length" type="integer" min="0" value="500" label="Minimum block length"/>
59 <param argument="--min-block-density" type="float" min="0" max="1" value="0.5" label="Minimum block density (0–1)"/> 60 <param argument="--min-block-density" type="float" min="0" max="1" value="0.5" label="Minimum block density (0–1)"/>
61 <param argument="--edit-distance" type="integer" min="0" max="2" value="0" label="Edit distance for pattern matching (0–2)"/>
60 62
61 <param argument="--out-win-repeats" type="boolean" truevalue="--out-win-repeats" falsevalue="" checked="false" label="Window repeat counts"/> 63 <param argument="--out-win-repeats" type="boolean" truevalue="--out-win-repeats" falsevalue="" checked="false" label="Window repeat counts"/>
62 <param argument="--out-gc" type="boolean" truevalue="--out-gc" falsevalue="" checked="false" label="Window GC"/> 64 <param argument="--out-gc" type="boolean" truevalue="--out-gc" falsevalue="" checked="false" label="Window GC"/>
63 <param argument="--out-entropy" type="boolean" truevalue="--out-entropy" falsevalue="" checked="false" label="Window Shannon entropy"/> 65 <param argument="--out-entropy" type="boolean" truevalue="--out-entropy" falsevalue="" checked="false" label="Window Shannon entropy"/>
64 <param argument="--out-matches" type="boolean" truevalue="--out-matches" falsevalue="" checked="false" label="Canonical/NonCanonical Matches"/> 66 <param argument="--out-matches" type="boolean" truevalue="--out-matches" falsevalue="" checked="false" label="Canonical/NonCanonical Matches"/>
156 <has_line_matching expression="\+\+\+ Path Summary Report \+\+\+"/> 158 <has_line_matching expression="\+\+\+ Path Summary Report \+\+\+"/>
157 <has_line_matching expression="\+\+\+ Assembly Summary Report \+\+\+"/> 159 <has_line_matching expression="\+\+\+ Assembly Summary Report \+\+\+"/>
158 <has_line_matching expression="\+\+\+ Telomere Statistics \+\+\+"/> 160 <has_line_matching expression="\+\+\+ Telomere Statistics \+\+\+"/>
159 <has_line_matching expression="\+\+\+ Chromosome Telomere Counts\+\+\+"/> 161 <has_line_matching expression="\+\+\+ Chromosome Telomere Counts\+\+\+"/>
160 <has_line_matching expression="\+\+\+ Chromosome Telomere/Gap Completeness\+\+\+"/> 162 <has_line_matching expression="\+\+\+ Chromosome Telomere/Gap Completeness\+\+\+"/>
163 </assert_contents>
164 </output>
165 </test>
166
167 <!-- 3) Edit distance 1: more variants detected -->
168 <test expect_num_outputs="2">
169 <param name="input_sequence" value="bTaeGut7_chr33_mat.fa.gz" ftype="fasta.gz"/>
170 <param name="canonical" value="TTAGGG"/>
171 <param name="patterns" value="TTAGGG,CCCTAA"/>
172 <param name="edit_distance" value="1"/>
173 <output name="terminal_telomeres">
174 <assert_contents>
175 <!-- p-arm telomere with extended start due to edit distance -->
176 <has_text text="chr33_mat&#9;442&#9;14354&#9;13912&#9;p&#9;"/>
177 <!-- q-arm telomere -->
178 <has_text text="chr33_mat&#9;4219967&#9;4246337&#9;26370&#9;q&#9;"/>
179 </assert_contents>
180 </output>
181 <output name="telo_report">
182 <assert_contents>
183 <has_line_matching expression="\+\+\+ Path Summary Report \+\+\+"/>
184 </assert_contents>
185 </output>
186 </test>
187
188 <!-- 4) Edit distance 2: maximum variants detected -->
189 <test expect_num_outputs="2">
190 <param name="input_sequence" value="bTaeGut7_chr33_mat.fa.gz" ftype="fasta.gz"/>
191 <param name="canonical" value="TTAGGG"/>
192 <param name="patterns" value="TTAGGG,CCCTAA"/>
193 <param name="edit_distance" value="2"/>
194 <output name="terminal_telomeres">
195 <assert_contents>
196 <!-- p-arm telomere extends to position 1 with edit distance 2 -->
197 <has_text text="chr33_mat&#9;1&#9;14354&#9;14353&#9;p&#9;"/>
198 <!-- q-arm telomere -->
199 <has_text text="chr33_mat&#9;4219967&#9;4246337&#9;26370&#9;q&#9;"/>
200 </assert_contents>
201 </output>
202 <output name="telo_report">
203 <assert_contents>
204 <has_line_matching expression="\+\+\+ Path Summary Report \+\+\+"/>
161 </assert_contents> 205 </assert_contents>
162 </output> 206 </output>
163 </test> 207 </test>
164 </tests> 208 </tests>
165 209
185 * ${input_sequence.name}.telo.report 229 * ${input_sequence.name}.telo.report
186 230
187 Key parameters: 231 Key parameters:
188 - -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. 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.
189 - -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. 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.
190 - -w / -s: window size / step (defaults 1000/500) 234 - -w / -s: window size / step (defaults 1000/500).
191 - -u / --ultra-fast: terminal scan only (default true); disabled automatically when -g/-e/-r/-m/-i are used. 235 - -u / --ultra-fast: terminal scan only (default true); disabled automatically when -g/-e/-r/-m/-i are used.
236 - -x / --edit-distance: Edit Hamming distance for pattern matching (0–2). Useful for identifying degenerate telomeric repeats (default 0).
192 ]]></help> 237 ]]></help>
193 238
194 <expand macro="citations"/> 239 <expand macro="citations"/>
195 </tool> 240 </tool>