Mercurial > repos > iuc > fastp
annotate macros.xml @ 15:a626e8c0e1ba draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 17a0a67dfbc7541a7fe3618cfbbb71d814042889
author | iuc |
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date | Fri, 15 Nov 2024 15:31:53 +0000 |
parents | ecb9f4854617 |
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rev | line source |
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0
988729b728f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
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1 <macros> |
14
ecb9f4854617
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit b76fe0b833d61c5161ed033ce1f57e3881bf336f
iuc
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2 <token name="@TOOL_VERSION@">0.24.0</token> |
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c59d48774d03
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 61d055a8abacf009e8afe2d72377e6769ad08f42
iuc
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3 <xml name="biotools"> |
c59d48774d03
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 61d055a8abacf009e8afe2d72377e6769ad08f42
iuc
parents:
10
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4 <xrefs> |
c59d48774d03
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 61d055a8abacf009e8afe2d72377e6769ad08f42
iuc
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5 <xref type="bio.tools"> |
c59d48774d03
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 61d055a8abacf009e8afe2d72377e6769ad08f42
iuc
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10
diff
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6 fastp |
c59d48774d03
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 61d055a8abacf009e8afe2d72377e6769ad08f42
iuc
parents:
10
diff
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7 </xref> |
c59d48774d03
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 61d055a8abacf009e8afe2d72377e6769ad08f42
iuc
parents:
10
diff
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8 </xrefs> |
c59d48774d03
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 61d055a8abacf009e8afe2d72377e6769ad08f42
iuc
parents:
10
diff
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9 </xml> |
5
3e2551a37201
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents:
3
diff
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10 <xml name="adapter_trimming_options"> |
3e2551a37201
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents:
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11 <section name="adapter_trimming_options" title="Adapter Trimming Options" expanded="False"> |
3e2551a37201
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
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12 <param name="disable_adapter_trimming" argument="-A" type="boolean" truevalue="-A" falsevalue="" checked="false" label="Disable adapter trimming" help="Adapter trimming is enabled by default. If this option is specified, adapter trimming is disabled."/> |
3e2551a37201
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents:
3
diff
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13 <expand macro="adapter_sequence" read_number="1" /> |
3e2551a37201
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
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3
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14 <yield /> |
3e2551a37201
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents:
3
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changeset
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15 </section> |
3e2551a37201
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents:
3
diff
changeset
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16 </xml> |
3e2551a37201
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents:
3
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17 |
3e2551a37201
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents:
3
diff
changeset
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18 <xml name="global_trimming_options"> |
3e2551a37201
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents:
3
diff
changeset
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19 <section name="global_trimming_options" title="Global trimming options" expanded="False"> |
3e2551a37201
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents:
3
diff
changeset
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20 <param name="trim_front1" argument="-f" type="integer" optional="true" label="Trim front for input 1" help="Trimming how many bases in front for read1, default is 0."/> |
3e2551a37201
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents:
3
diff
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21 <param name="trim_tail1" argument="-t" type="integer" optional="true" label="Trim tail for input 1" help="Trimming how many bases in tail for read1, default is 0."/> |
3e2551a37201
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents:
3
diff
changeset
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22 <yield/> |
3e2551a37201
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents:
3
diff
changeset
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23 </section> |
3e2551a37201
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents:
3
diff
changeset
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24 </xml> |
3e2551a37201
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents:
3
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25 |
3e2551a37201
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents:
3
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changeset
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26 <xml name="global_trimming_options_paired"> |
3e2551a37201
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents:
3
diff
changeset
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27 <expand macro="global_trimming_options"> |
3e2551a37201
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents:
3
diff
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28 <param name="trim_front2" argument="-F" type="integer" optional="true" label="Trim front for input 2" help="Trimming how many bases in front for read2. If it's not specified, it will follow read1's settings."/> |
3e2551a37201
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents:
3
diff
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29 <param name="trim_tail2" argument="-T" type="integer" optional="true" label="Trim tail for input 2" help="Trimming how many bases in tail for read2. If it's not specified, it will follow read1's settings."/> |
3e2551a37201
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents:
3
diff
changeset
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30 </expand> |
3e2551a37201
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents:
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diff
changeset
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31 </xml> |
3e2551a37201
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents:
3
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32 |
3e2551a37201
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents:
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33 <xml name="adapter_sequence" token_read_number="1"> |
11
c59d48774d03
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 61d055a8abacf009e8afe2d72377e6769ad08f42
iuc
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34 <param argument="--adapter_sequence@READ_NUMBER@" type="text" optional="true" label="Adapter sequence for input @READ_NUMBER@" help="The adapter for read@READ_NUMBER@. For SE data, if not specified, the adapter will be auto-detected. For PE data, this is used if R1/R2 are found not overlapped."> |
0
988729b728f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
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35 <sanitizer> |
988729b728f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
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36 <valid> |
988729b728f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
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37 <add value="A"/> |
988729b728f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
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38 <add value="T"/> |
988729b728f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
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39 <add value="C"/> |
988729b728f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
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40 <add value="G"/> |
988729b728f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
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41 </valid> |
988729b728f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
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42 </sanitizer> |
988729b728f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
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43 </param> |
988729b728f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
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44 </xml> |
5
3e2551a37201
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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45 |
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dbfc505896e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
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46 <xml name="merge_reads"> |
dbfc505896e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
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47 <conditional name="merge_reads"> |
dbfc505896e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
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48 <param argument="--merge" type="select" label="Merge forward and revese reads?"> |
dbfc505896e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
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49 <option value="">No</option> |
dbfc505896e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
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50 <option value="--merge">Yes</option> |
dbfc505896e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
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51 </param> |
dbfc505896e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
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52 <when value="--merge"> |
dbfc505896e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
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53 <param argument="--include_unmerged" type="boolean" truevalue="--include_unmerged" falsevalue="" checked="false" label="Include unmerged outputs into merged output file" /> |
dbfc505896e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
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54 </when> |
dbfc505896e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
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55 <when value="" /> |
dbfc505896e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
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56 </conditional> |
dbfc505896e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
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57 </xml> |
dbfc505896e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
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58 |
12
d60c3f704da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6b8fbd9db12329e2f49eee672b185015c3e35d4f
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59 <xml name="detect_adapter_for_pe"> |
d60c3f704da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6b8fbd9db12329e2f49eee672b185015c3e35d4f
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60 <param argument="--detect_adapter_for_pe" type="boolean" truevalue="--detect_adapter_for_pe" falsevalue="" checked="false" label="Adapter sequence auto-detection for paired-end" /> |
d60c3f704da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6b8fbd9db12329e2f49eee672b185015c3e35d4f
iuc
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61 </xml> |
d60c3f704da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6b8fbd9db12329e2f49eee672b185015c3e35d4f
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62 |
5
3e2551a37201
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
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63 <xml name="in" token_read_number="1" token_argument="-i"> |
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a626e8c0e1ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 17a0a67dfbc7541a7fe3618cfbbb71d814042889
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64 <param name="in@READ_NUMBER@" argument="@ARGUMENT@" type="data" format="fastqsanger,fastqsanger.gz" label="Input @READ_NUMBER@" help="Input FASTQ file #@READ_NUMBER@"/> |
0
988729b728f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
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65 </xml> |
5
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
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66 |
0
988729b728f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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67 <xml name="poly_g_min_len"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 61d055a8abacf009e8afe2d72377e6769ad08f42
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68 <param argument="--poly_g_min_len" type="integer" optional="true" label="PolyG minimum length" |
0
988729b728f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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69 help="The minimum length to detect polyG in the read tail. 10 by default."/> |
988729b728f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
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70 </xml> |
15
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 17a0a67dfbc7541a7fe3618cfbbb71d814042889
iuc
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71 |
a626e8c0e1ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 17a0a67dfbc7541a7fe3618cfbbb71d814042889
iuc
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72 <xml name="format_actions" token_read_number="1" token_forward_reverse="forward"> |
a626e8c0e1ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 17a0a67dfbc7541a7fe3618cfbbb71d814042889
iuc
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73 <actions> |
a626e8c0e1ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 17a0a67dfbc7541a7fe3618cfbbb71d814042889
iuc
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74 <conditional name="single_paired.single_paired_selector"> |
a626e8c0e1ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 17a0a67dfbc7541a7fe3618cfbbb71d814042889
iuc
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75 <when value="paired"> |
a626e8c0e1ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 17a0a67dfbc7541a7fe3618cfbbb71d814042889
iuc
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76 <action type="format"> |
a626e8c0e1ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 17a0a67dfbc7541a7fe3618cfbbb71d814042889
iuc
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77 <option type="from_param" name="single_paired.in@READ_NUMBER@" param_attribute="ext" /> |
a626e8c0e1ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 17a0a67dfbc7541a7fe3618cfbbb71d814042889
iuc
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78 </action> |
a626e8c0e1ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 17a0a67dfbc7541a7fe3618cfbbb71d814042889
iuc
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79 </when> |
a626e8c0e1ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 17a0a67dfbc7541a7fe3618cfbbb71d814042889
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80 <when value="paired_collection"> |
a626e8c0e1ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 17a0a67dfbc7541a7fe3618cfbbb71d814042889
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81 <action type="format"> |
a626e8c0e1ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 17a0a67dfbc7541a7fe3618cfbbb71d814042889
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82 <option type="from_param" name="single_paired.paired_input" param_attribute="@FORWARD_REVERSE@.ext" /> |
a626e8c0e1ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 17a0a67dfbc7541a7fe3618cfbbb71d814042889
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83 </action> |
a626e8c0e1ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 17a0a67dfbc7541a7fe3618cfbbb71d814042889
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84 </when> |
a626e8c0e1ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 17a0a67dfbc7541a7fe3618cfbbb71d814042889
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85 </conditional> |
a626e8c0e1ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 17a0a67dfbc7541a7fe3618cfbbb71d814042889
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86 </actions> |
a626e8c0e1ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 17a0a67dfbc7541a7fe3618cfbbb71d814042889
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87 </xml> |
a626e8c0e1ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 17a0a67dfbc7541a7fe3618cfbbb71d814042889
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88 </macros> |