Mercurial > repos > iuc > hisat2
annotate hisat2.xml @ 7:5ba8e317529a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
author | iuc |
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date | Sat, 21 Jan 2017 15:42:34 -0500 |
parents | 5f4da9ec47c7 |
children | 4d0a3173cde0 |
rev | line source |
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5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
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1 <?xml version="1.0"?> |
7
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
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2 <tool id="hisat2" name="HISAT2" version="2.0.3.2"> |
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5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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3 <description>A fast and sensitive alignment program</description> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
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4 <macros> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
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5 <import>hisat2_macros.xml</import> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
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6 </macros> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
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7 <requirements> |
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b1e25f9b5eab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 9a9d44116b21d9a155b5cc274475e78c14915059
iuc
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8 <!-- Conda dependency --> |
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2d449a1bb5ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit f33b04533bca91242b8a0a4077e1d593f5a874e0
iuc
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9 <requirement type="package" version="2.0.3">hisat2</requirement> |
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1eb21dccc2fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
parents:
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10 <requirement type="package" version="2.0.3">hisat</requirement> |
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5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
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11 <requirement type="package" version="1.2">samtools</requirement> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
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12 </requirements> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
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13 <stdio> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
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14 <regex match="hisat2-align exited with value 1" source="both" level="fatal"/> |
3
b1e25f9b5eab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 9a9d44116b21d9a155b5cc274475e78c14915059
iuc
parents:
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15 <regex match="hisat2: not found" source="both" level="fatal"/> |
0
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
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16 <exit_code range="1:" /> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
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17 </stdio> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
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18 <version_command>hisat2 --version</version_command> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
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19 <command> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
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20 <![CDATA[ |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
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21 #if str($spliced_options.spliced_options_selector) == "advanced" and str($spliced_options.known_splice_gtf) != 'None': |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
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22 ln -s "${spliced_options.known_splice_gtf}" splice_sites.gtf && |
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1eb21dccc2fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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23 hisat2_extract_splice_sites.py splice_sites.gtf > splice_sites.txt && |
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5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
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changeset
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24 #end if |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
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25 #if $reference_genome.reference_genome_source == "history": |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
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26 ln -s "$reference_genome.history_item" genome.fa && |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
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27 hisat2-build genome.fa genome && |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
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28 #set index_path = 'genome' |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
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29 #else: |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
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30 #set index_path = $reference_genome.index.fields.path |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
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31 #end if |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
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32 hisat2 -p \${GALAXY_SLOTS:-1} -x "${index_path}" |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
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33 #if str($input_format.paired.paired_selector) == 'paired': |
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b1e25f9b5eab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 9a9d44116b21d9a155b5cc274475e78c14915059
iuc
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34 -1 "${input_format.paired.reads_f}" -2 "${input_format.paired.reads_r}" |
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5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
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35 @paired_end_options@ |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
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36 #else if str($input_format.paired.paired_selector) == 'paired_collection': |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
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37 -1 "${input_format.paired.reads.forward}" -2 "${input_format.paired.reads.reverse}" |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
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38 @paired_end_options@ |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
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39 #else: |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
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40 -U "${input_format.paired.reads}" |
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5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
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41 #if str( $input_format.paired.unaligned_file ) == "true": |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
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42 --un '$output_unaligned_reads_l' |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
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43 #end if |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
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44 #if str( $input_format.paired.aligned_file ) == "true": |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
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45 --al '$output_aligned_reads_l' |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
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46 #end if |
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5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
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47 #end if |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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48 #if $input_format.input_format_selector == 'fasta': |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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49 -f |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
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50 #end if |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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51 #if $max_primary: |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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52 -k ${max_primary} |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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53 #end if |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
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54 #if str($input_options.input_options_selector) == "advanced": |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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55 #if int( $input_options.skip ) > 0: |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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56 -s ${input_options.skip} |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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57 #end if |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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58 #if int( $input_options.stop_after ) > 0: |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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59 -u ${input_options.stop_after} |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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60 #end if |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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61 -5 ${input_options.trim_five} -3 ${input_options.trim_three} |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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62 #end if |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
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63 #if str($scoring_options.scoring_options_selector) == "advanced": |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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64 --ma ${scoring_options.match_bonus} --np ${scoring_options.ambiguous_penalty} |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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65 --mp ${scoring_options.max_mismatch},${scoring_options.min_mismatch} |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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66 --rdg ${scoring_options.read_open_penalty},${scoring_options.read_extend_penalty} |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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67 --rfg ${scoring_options.ref_open_penalty},${scoring_options.ref_extend_penalty} |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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68 --sp ${scoring_options.soft_clip_penalty_max},${scoring_options.soft_clip_penalty_min} |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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69 --score-min ${scoring_options.function_type},${scoring_options.constant_term},${scoring_options.coefficient} |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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70 #end if |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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71 #if str($alignment_options.alignment_options_selector) == "advanced": |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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72 --n-ceil ${alignment_options.function_type},${alignment_options.constant_term},${alignment_options.coefficient} |
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c37b4554f794
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit a2aaa7c9fe7b343f95450ec428250317696a9fb7
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73 ${alignment_options.skip_forward} ${alignment_options.skip_reverse} ${alignment_options.ignore_quals} |
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5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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74 #end if |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
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75 #if str($spliced_options.spliced_options_selector) == "advanced": |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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76 --pen-cansplice ${spliced_options.canonical_penalty} --pen-noncansplice ${spliced_options.noncanonical_penalty} |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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77 --pen-canintronlen ${spliced_options.function_type},${spliced_options.constant_term},${spliced_options.coefficient} |
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78 --pen-noncanintronlen ${spliced_options.nc_function_type},${spliced_options.nc_constant_term},${spliced_options.nc_coefficient} |
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79 #if str($spliced_options.known_splice_gtf) != 'None': |
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80 --known-splicesite-infile splice_sites.txt |
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81 #end if |
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82 ${spliced_options.no_spliced_alignment} |
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83 --min-intronlen ${spliced_options.min_intron} |
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84 --max-intronlen ${spliced_options.max_intron} |
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85 ${spliced_options.tma} |
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86 @strandedness_parameters@ |
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87 #end if |
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88 #if str($paired_options.paired_options_selector) == "advanced": |
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89 --minins ${paired_options.minins} --maxins ${paired_options.maxins} ${paired_options.no_mixed} ${paired_options.no_discordant} |
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90 ${paired_options.dovetail} ${paired_options.contain} ${paired_options.overlap} |
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91 #end if |
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92 | samtools sort - -@ \${GALAXY_SLOTS:-2} -l 6 -o hsbam > "${output_alignments}" |
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93 |
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94 ## Rename any output fastq files |
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95 #if str($input_format.paired.paired_selector) == 'paired' or str($input_format.paired.paired_selector) == 'paired_collection': |
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96 #if $output_unaligned_reads_l and $output_unaligned_reads_r: |
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97 #set left = str($output_unaligned_reads_l).replace(".dat", ".1.dat") |
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98 #set right = str($output_unaligned_reads_l).replace(".dat", ".2.dat") |
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99 && mv '${left}' '${output_unaligned_reads_l}' |
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100 && mv '${right}' '${output_unaligned_reads_r}' |
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101 #end if |
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102 #if $output_aligned_reads_l and $output_aligned_reads_r: |
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103 #set left = str($output_aligned_reads_l).replace(".dat", ".1.dat") |
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104 #set right = str($output_aligned_reads_l).replace(".dat", ".2.dat") |
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105 && mv '${left}' '${output_aligned_reads_l}' |
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106 && mv '${right}' '${output_aligned_reads_r}' |
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107 #end if |
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108 #end if |
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109 ]]> |
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110 </command> |
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111 <inputs> |
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112 <conditional name="input_format"> |
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113 <param label="Input data format" name="input_format_selector" type="select"> |
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114 <option selected="true" value="fastq">FASTQ</option> |
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115 <option value="fasta">FASTA</option> |
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116 </param> |
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117 <when value="fasta"> |
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118 <expand ftype="fasta" macro="paired_input_conditional" /> |
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119 </when> |
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120 <when value="fastq"> |
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121 <expand ftype="fastq" macro="paired_input_conditional" /> |
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122 </when> |
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123 </conditional> |
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124 <conditional name="reference_genome"> |
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125 <param help="Built-in references were created using default options" label="Source for the reference genome to align against" name="reference_genome_source" type="select"> |
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126 <option selected="True" value="indexed">Use a built-in genome</option> |
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127 <option value="history">Use a genome from history</option> |
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128 </param> |
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129 <when value="indexed"> |
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130 <param help="If your genome of interest is not listed, contact the Galaxy team" label="Select a reference genome" name="index" type="select"> |
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131 <options from_data_table="hisat2_indexes"> |
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132 <filter column="2" type="sort_by" /> |
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133 <validator message="No genomes are available for the selected input dataset" type="no_options" /> |
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134 </options> |
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135 </param> |
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136 </when> |
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137 <when value="history"> |
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138 <param format="fasta" label="Select the reference genome" name="history_item" type="data" /> |
0
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139 </when> |
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140 </conditional> |
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141 <param argument="-k" name="max_primary" optional="True" type="integer" value="5" help="Search for at most K distinct, primary alignments for each read. Primary alignments mean alignments whose alignment score is equal or higher than any other alignments. The search terminates when it can't find more distinct valid alignments, or when it finds K, whichever happens first." label="Primary alignments" /> |
0
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142 <conditional name="alignment_options"> |
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143 <param label="Alignment options" name="alignment_options_selector" type="select"> |
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144 <option value="defaults">Use default values</option> |
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145 <option value="advanced">Specify alignment parameters</option> |
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146 </param> |
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147 <when value="defaults" /> |
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148 <when value="advanced"> |
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149 <expand macro="function" helptext="Sets a function governing the maximum number of ambiguous characters" /> |
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150 <param argument="--ignore-quals" falsevalue="" help="When calculating a mismatch penalty, always consider the quality value at the mismatched position to be the highest possible, regardless of the actual value. I.e. input is treated as though all quality values are high. This is also the default behavior when the input doesn't specify quality values." label="Ignore quality values" name="ignore_quals" truevalue="--ignore-quals" type="boolean" /> |
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151 <param argument="--nofw" falsevalue="" help="If --nofw is specified, hisat will not attempt to align unpaired reads to the forward (Watson) reference strand. In paired-end mode, --nofw and --norc pertain to the fragments; i.e. specifying --nofw causes hisat to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand." label="Skip forward strand of reference" name="skip_forward" truevalue="--nofw" type="boolean" /> |
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152 <param argument="--norc" falsevalue="" help="If --norc is specified, hisat will not attempt to align unpaired reads against the reverse-complement (Crick) reference strand. In paired-end mode, --nofw and --norc pertain to the fragments; i.e. specifying --nofw causes hisat to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand." label="Skip reference strand of reference" name="skip_reverse" truevalue="--norc" type="boolean" /> |
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153 </when> |
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154 </conditional> |
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155 <conditional name="input_options"> |
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156 <param label="Input options" name="input_options_selector" type="select"> |
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157 <option value="defaults">Use default values</option> |
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158 <option value="advanced">Specify input parameters</option> |
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159 </param> |
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160 <when value="defaults" /> |
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161 <when value="advanced"> |
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162 <param argument="-s" min="0" label="Skip the first N reads or pairs in the input" name="skip" type="integer" value="0" /> |
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163 <param argument="-u" min="0" help="Align the first N reads or read pairs from the input (after the first N reads or pairs have been skipped), then stop." label="Stop after aligning N reads" name="stop_after" type="integer" value="0" /> |
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164 <param argument="-5" min="0" help="Trim N bases from 5' (left) end of each read before alignment" label="Trim 5' end" name="trim_five" type="integer" value="0" /> |
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165 <param argument="-3" min="0" help="Trim N bases from 3' (right) end of each read before alignment" label="Trim 3' end" name="trim_three" type="integer" value="0" /> |
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166 </when> |
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167 </conditional> |
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168 <conditional name="scoring_options"> |
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169 <param label="Scoring options" name="scoring_options_selector" type="select"> |
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170 <option value="defaults">Use default values</option> |
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171 <option value="advanced">Specify scoring parameters</option> |
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172 </param> |
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173 <when value="defaults" /> |
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174 <when value="advanced"> |
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175 <expand macro="function" helptext="Sets a function governing the minimum alignment score needed for an alignment to be considered "valid" (i.e. good enough to report)." /> |
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176 <param argument="--ma" help="In local mode N is added to the alignment score for each position where a read character aligns to a reference character and the characters match. Not used in end-to-end mode" label="Set match bonus" name="match_bonus" type="integer" value="2" /> |
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177 <param argument="--mp" help="Sets the maximum mismatch penalty. A number less than or equal to MX and greater than or equal to MN is subtracted from the alignment score for each position where a read character aligns to a reference character, the characters do not match, and neither is an N. If --ignore-quals is specified, the number subtracted quals MX. Otherwise, the number subtracted is MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) ) where Q is the Phred quality value." label="Maximum mismatch penalty" name="max_mismatch" type="integer" value="6" /> |
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178 <param argument="--mp" help="Sets the minimum mismatch penalty. A number less than or equal to MX and greater than or equal to MN is subtracted from the alignment score for each position where a read character aligns to a reference character, the characters do not match, and neither is an N. If --ignore-quals is specified, the number subtracted quals MX. Otherwise, the number subtracted is MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) ) where Q is the Phred quality value." label="Minimum mismatch penalty" name="min_mismatch" type="integer" value="2" /> |
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179 <param argument="--np" help="Sets penalty for positions where the read, reference, or both, contain an ambiguous character such as N" label="Ambiguous read penalty" name="ambiguous_penalty" type="integer" value="1" /> |
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180 <param argument="--sp" help="Sets the maximum (MX) penalty for soft-clipping per base. A number less than or equal to MX and greater than or equal to MN is subtracted from the alignment score for each position. The number subtracted is MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) ) where Q is the Phred quality value." label="Maximum soft-clipping penalty" name="soft_clip_penalty_max" type="integer" value="2" /> |
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181 <param argument="--sp" help="Sets the minimum (MN) penalty for soft-clipping per base. A number less than or equal to MX and greater than or equal to MN is subtracted from the alignment score for each position. The number subtracted is MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) ) where Q is the Phred quality value." label="Minimum soft-clipping penalty" name="soft_clip_penalty_min" type="integer" value="1" /> |
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182 <param argument="--rdg" help="A read gap of length N gets a penalty of [open_penalty] + N * [extend_penalty]" label="Read gap open penalty." name="read_open_penalty" type="integer" value="5" /> |
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183 <param argument="--rdg" help="A read gap of length N gets a penalty of [open_penalty] + N * [extend_penalty]" label="Read gap extend penalty." name="read_extend_penalty" type="integer" value="3" /> |
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184 <param argument="--rfg" help="A reference gap of length N gets a penalty of [open_penalty] + N * [extend_penalty]" label="Reference gap open penalty." name="ref_open_penalty" type="integer" value="5" /> |
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185 <param argument="--rfg" help="A reference gap of length N gets a penalty of [open_penalty] + N * [extend_penalty]" label="Reference gap extend penalty." name="ref_extend_penalty" type="integer" value="3" /> |
0
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186 </when> |
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187 </conditional> |
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188 <conditional name="spliced_options"> |
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189 <param label="Spliced alignment parameters" name="spliced_options_selector" type="select"> |
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190 <option value="defaults">Use default values</option> |
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191 <option value="advanced">Specify spliced alignment parameters</option> |
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192 </param> |
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193 <when value="defaults" /> |
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194 <when value="advanced"> |
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195 <param label="Penalty for canonical splice sites" name="canonical_penalty" type="integer" value="0" /> |
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196 <param label="Penalty for non-canonical splice sites" name="noncanonical_penalty" type="integer" value="3" /> |
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197 <param display="radio" label="Penalty for long introns with canonical splice sites" name="function_type" type="select"> |
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198 <option value="C">Constant</option> |
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199 <option value="L">Linear [f(x) = y + z * x]</option> |
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200 <option value="S">Square root [f(x) = y + z * x²]</option> |
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201 <option value="G">Natural logarithm [f(x) = y + z * log(x)]</option> |
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202 </param> |
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203 <param help="Constant term for long canonical introns" label="Constant term (y)" name="constant_term" type="integer" value="0" /> |
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204 <param help="Coefficient for long canonical introns" label="Coefficient (z)" name="coefficient" type="integer" value="0" /> |
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205 <param display="radio" label="Penalty for long introns with noncanonical splice sites." name="nc_function_type" type="select"> |
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206 <option value="C">Constant</option> |
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207 <option value="L">Linear [f(x) = y + z * x]</option> |
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208 <option value="S">Square root [f(x) = y + z * x²]</option> |
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209 <option selected="True" value="G">Natural logarithm [f(x) = y + z * log(x)]</option> |
0
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210 </param> |
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211 <param help="Constant term for long non-canonical introns" label="Constant term (y)" name="nc_constant_term" type="integer" value="-8" /> |
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212 <param help="Coefficient for long non-canonical introns" label="Coefficient (z)" name="nc_coefficient" type="integer" value="1" /> |
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213 <param label="Minimum intron length" name="min_intron" type="integer" value="20" /> |
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214 <param label="Maximum intron length" name="max_intron" type="integer" value="500000" /> |
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215 <param argument="--rna-strandness" name="rna_strandness" type="select" label="Specify strand-specific information" |
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216 help="'F' means a read corresponds to a transcript. 'R' means a read corresponds to the reverse complemented counterpart of a transcript."> |
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217 <option value="">FR Unstranded</option> |
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218 <option value="R">First Strand (R/RF)</option> |
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219 <option value="F">Second Strand (F/FR)</option> |
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220 </param> |
2
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221 <param argument="--no-spliced-alignment" name="no_spliced_alignment" type="boolean" truevalue="--no-spliced-alignment" falsevalue="" label="Disable spliced alignment" /> |
0
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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222 <param format="gtf" label="GTF file with known splice sites" name="known_splice_gtf" optional="True" type="data" /> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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223 <param display="radio" label="Transcriptome assembly reporting" name="tma" type="select"> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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224 <option value="">Use default reporting.</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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225 <option value="--tmo">Report only those alignments within known transcripts.</option> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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226 <option value="--dta">Report alignments tailored for transcript assemblers including StringTie.</option> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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227 <option value="--dta-cufflinks">Report alignments tailored specifically for Cufflinks.</option> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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228 </param> |
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229 </when> |
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230 </conditional> |
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231 <conditional name="paired_options"> |
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232 <param label="Paired alignment parameters" name="paired_options_selector" type="select"> |
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233 <option value="defaults">Use default values</option> |
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234 <option value="advanced">Specify paired alignment parameters</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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235 </param> |
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236 <when value="defaults" /> |
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237 <when value="advanced"> |
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238 <param argument="--minins" help="The minimum fragment length for valid paired-end alignments. 0 sets no minimum." label="Minimum fragment length" name="minins" type="integer" value="0" /> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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239 <param argument="--maxins" help="The maximum fragment length for valid paired-end alignments" label="Maximum fragment length" name="maxins" type="integer" value="500" /> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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240 <param argument="--no-mixed" falsevalue="" help="By default, when hisat2 cannot find a concordant or discordant alignment for a pair, it then tries to find alignments for the individual mates" label="Disable finding alignments for individual mates." name="no_mixed" truevalue="--no-mixed" type="boolean" /> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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241 <param argument="--no-discordant" falsevalue="" help="By default, hisat2 looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints" label="Disable looking for discordant alignments." name="no_discordant" truevalue="--no-discordant" type="boolean" /> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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242 <param argument="--dovetail" falsevalue="" help="If the mates "dovetail", that is if one mate alignment extends past the beginning of the other such that the wrong mate begins upstream, consider that to be concordant." label="Mates not dovetail" name="dovetail" truevalue="--dovetail" type="boolean" /> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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243 <param argument="--no-contain" falsevalue="" help="If one mate alignment contains the other, consider that to be non-concordant." label="Mates cannot contain others" name="contain" truevalue="--no-contain" type="boolean" /> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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244 <param argument="--no-overlap" falsevalue="" help="If one mate alignment overlaps the other at all, consider that to be non-concordant." label="Mates cannot overlap" name="overlap" truevalue="--no-overlap" type="boolean" /> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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245 </when> |
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246 </conditional> |
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247 </inputs> |
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248 <outputs> |
3
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249 <data format="bam" name="output_alignments"> |
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250 <actions> |
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251 <conditional name="reference_genome.reference_genome_source"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 9a9d44116b21d9a155b5cc274475e78c14915059
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252 <when value="indexed"> |
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253 <action type="metadata" name="dbkey"> |
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254 <option type="from_data_table" name="hisat2_indexes" column="1" offset="0"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 9a9d44116b21d9a155b5cc274475e78c14915059
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255 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> |
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256 <filter type="param_value" ref="reference_genome.index" column="0"/> |
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257 </option> |
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258 </action> |
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259 </when> |
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260 <when value="history"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 9a9d44116b21d9a155b5cc274475e78c14915059
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261 <action type="metadata" name="dbkey"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 9a9d44116b21d9a155b5cc274475e78c14915059
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262 <option type="from_param" name="reference_genome.history_item" param_attribute="dbkey" /> |
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263 </action> |
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264 </when> |
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265 </conditional> |
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266 </actions> |
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267 </data> |
7
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268 <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" > |
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269 <filter>input_format['paired']['unaligned_file'] is True</filter> |
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270 <actions> |
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271 <conditional name="input_format.paired.paired_selector"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
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272 <when value="single"> |
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273 <action type="format"> |
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274 <option type="from_param" name="input_format.paired.reads" param_attribute="ext" /> |
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275 </action> |
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276 </when> |
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277 <when value="paired"> |
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278 <action type="format"> |
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279 <option type="from_param" name="input_format.paired.reads_f" param_attribute="ext" /> |
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280 </action> |
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281 </when> |
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282 <when value="paired_collection"> |
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283 <action type="format"> |
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284 <option type="from_param" name="input_format.paired.reads" param_attribute="forward.ext" /> |
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285 </action> |
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286 </when> |
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287 </conditional> |
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288 </actions> |
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289 </data> |
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290 <data format="fastqsanger" name="output_unaligned_reads_r" label="${tool.name} on ${on_string}: unaligned reads (R)" > |
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291 <filter>input_format['paired']['unaligned_file'] is True and input_format['paired']['paired_selector'] != 'single'</filter> |
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292 <actions> |
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293 <conditional name="input_format.paired.paired_selector"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
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294 <when value="paired"> |
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295 <action type="format"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
296 <option type="from_param" name="input_format.paired.reads_r" param_attribute="ext" /> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
297 </action> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
298 </when> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
299 <when value="paired_collection"> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
300 <action type="format"> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
301 <option type="from_param" name="input_format.paired.reads" param_attribute="forward.ext" /> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
302 </action> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
303 </when> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
304 </conditional> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
305 </actions> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
306 </data> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
307 <data format="fastqsanger" name="output_aligned_reads_l" label="${tool.name} on ${on_string}: aligned reads${' (L)' if str($input_format.paired.paired_selector) != 'single' else ''}" > |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
308 <filter>input_format['paired']['aligned_file'] is True</filter> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
309 <actions> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
310 <conditional name="input_format.paired.paired_selector"> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
311 <when value="single"> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
312 <action type="format"> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
313 <option type="from_param" name="input_format.paired.reads" param_attribute="ext" /> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
314 </action> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
315 </when> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
316 <when value="paired"> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
317 <action type="format"> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
318 <option type="from_param" name="input_format.paired.reads_f" param_attribute="ext" /> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
319 </action> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
320 </when> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
321 <when value="paired_collection"> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
322 <action type="format"> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
323 <option type="from_param" name="input_format.paired.reads" param_attribute="forward.ext" /> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
324 </action> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
325 </when> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
326 </conditional> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
327 </actions> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
328 </data> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
329 <data format="fastqsanger" name="output_aligned_reads_r" label="${tool.name} on ${on_string}: aligned reads (R)" > |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
330 <filter>input_format['paired']['aligned_file'] is True and input_format['paired']['paired_selector'] != 'single'</filter> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
331 <actions> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
332 <conditional name="input_format.paired.paired_selector"> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
333 <when value="paired"> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
334 <action type="format"> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
335 <option type="from_param" name="input_format.paired.reads_r" param_attribute="ext" /> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
336 </action> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
337 </when> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
338 <when value="paired_collection"> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
339 <action type="format"> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
340 <option type="from_param" name="input_format.paired.reads" param_attribute="forward.ext" /> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
341 </action> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
342 </when> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
343 </conditional> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
344 </actions> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
345 </data> |
0
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
346 </outputs> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
347 <tests> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
348 <test> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
349 <param name="input_format_selector" value="fastq" /> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
350 <param name="paired_selector" value="paired" /> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
351 <param name="reference_genome_source" value="history" /> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
352 <param ftype="fasta" name="history_item" value="phiX.fa" /> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
353 <param ftype="fastqsanger" name="reads_f" value="hisat_input_1_forward.fastq" /> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
354 <param ftype="fastqsanger" name="reads_r" value="hisat_input_1_reverse.fastq" /> |
4
2d449a1bb5ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit f33b04533bca91242b8a0a4077e1d593f5a874e0
iuc
parents:
3
diff
changeset
|
355 <output file="hisat_output_1.bam" ftype="bam" name="output_alignments" lines_diff="2" /> |
0
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
356 </test> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
357 <test> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
358 <param name="input_format_selector" value="fastq" /> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
359 <param name="paired_selector" value="paired" /> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
360 <param name="reference_genome_source" value="history" /> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
361 <param ftype="fasta" name="history_item" value="phiX.fa" /> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
362 <param name="input_options_selector" value="advanced" /> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
363 <param name="trim_three" value="15" /> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
364 <param name="trim_five" value="15" /> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
365 <param ftype="fastqsanger" name="reads_f" value="hisat_input_2_forward.fastq" /> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
366 <param ftype="fastqsanger" name="reads_r" value="hisat_input_2_reverse.fastq" /> |
4
2d449a1bb5ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit f33b04533bca91242b8a0a4077e1d593f5a874e0
iuc
parents:
3
diff
changeset
|
367 <output file="hisat_output_2.bam" ftype="bam" name="output_alignments" lines_diff="2" /> |
0
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
368 </test> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
369 <test> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
370 <param name="input_format_selector" value="fastq" /> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
371 <param name="paired_selector" value="paired" /> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
372 <param name="reference_genome_source" value="history" /> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
373 <param name="history_item" value="phiX.fa" ftype="fasta" /> |
5bafe7d7a55e
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374 <param name="input_options_selector" value="advanced" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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375 <param name="trim_three" value="15" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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376 <param name="trim_five" value="15" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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377 <param name="reads_f" ftype="fastqsanger" value="hisat_input_2_forward.fastq" /> |
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378 <param name="reads_r" ftype="fastqsanger" value="hisat_input_2_reverse.fastq" /> |
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379 <param name="paired_end_options_selector" value="advanced" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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380 <param name="no_mixed" value="True" /> |
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381 <param name="no_discordant" value="True" /> |
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382 <output name="output_alignments" ftype="bam" file="hisat_output_3.bam" lines_diff="2" /> |
0
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383 </test> |
7
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384 <test><!-- testing unaligned output (single dataset) --> |
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385 <param name="input_format_selector" value="fasta" /> |
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386 <param name="paired_selector" value="single" /> |
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387 <param name="reference_genome_source" value="history" /> |
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388 <param name="history_item" value="phiX.fa" ftype="fasta" /> |
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389 <param name="unaligned_file" value="true" /> |
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390 <param name="aligned_file" value="true" /> |
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391 <param name="reference_genome_source" value="history" /> |
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392 <param name="history_item" value="phiX.fa" ftype="fasta" /> |
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393 <param name="reads" value="test_unaligned_reads.fasta" ftype="fasta" /> |
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394 |
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395 <output name="output_unaligned_reads_l" file="test_unaligned_reads.fasta" /> |
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396 </test> |
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397 |
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398 <test> |
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399 <param name="input_format_selector" value="fasta" /> |
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400 <param name="paired_selector" value="paired" /> |
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401 <param name="reference_genome_source" value="history" /> |
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402 <param name="history_item" value="phiX.fa" ftype="fasta" /> |
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403 <param name="unaligned_file" value="true" /> |
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404 <param name="aligned_file" value="true" /> |
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405 <param name="reference_genome_source" value="history" /> |
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406 <param name="history_item" value="phiX.fa" ftype="fasta" /> |
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407 <param name="reads_f" value="test_unaligned_reads.fasta" ftype="fasta" /> |
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408 <param name="reads_r" value="test_unaligned_reads.fasta" ftype="fasta" /> |
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409 |
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410 <output name="output_unaligned_reads_l" file="test_unaligned_reads.fasta" /> |
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411 <output name="output_unaligned_reads_r" file="test_unaligned_reads.fasta" /> |
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412 </test> |
0
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413 </tests> |
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414 <help> |
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415 <![CDATA[ |
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416 Introduction |
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417 ============ |
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418 |
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419 What is HISAT? |
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420 -------------- |
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421 |
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422 `HISAT <http://ccb.jhu.edu/software/hisat>`__ is a fast and sensitive |
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423 spliced alignment program. As part of HISAT, we have developed a new |
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424 indexing scheme based on the Burrows-Wheeler transform |
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425 (`BWT <http://en.wikipedia.org/wiki/Burrows-Wheeler_transform>`__) and |
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426 the `FM index <http://en.wikipedia.org/wiki/FM-index>`__, called |
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427 hierarchical indexing, that employs two types of indexes: (1) one global |
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428 FM index representing the whole genome, and (2) many separate local FM |
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429 indexes for small regions collectively covering the genome. Our |
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430 hierarchical index for the human genome (about 3 billion bp) includes |
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431 ~48,000 local FM indexes, each representing a genomic region of |
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432 ~64,000bp. As the basis for non-gapped alignment, the FM index is |
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433 extremely fast with a low memory footprint, as demonstrated by |
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434 `Bowtie <http://bowtie-bio.sf.net>`__. In addition, HISAT provides |
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435 several alignment strategies specifically designed for mapping different |
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436 types of RNA-seq reads. All these together, HISAT enables extremely fast |
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437 and sensitive alignment of reads, in particular those spanning two exons |
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438 or more. As a result, HISAT is much faster >50 times than |
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439 `TopHat2 <http://ccb.jhu.edu/software/tophat>`__ with better alignment |
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440 quality. Although it uses a large number of indexes, the memory |
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441 requirement of HISAT is still modest, approximately 4.3 GB for human. |
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442 HISAT uses the `Bowtie2 <http://bowtie-bio.sf.net/bowtie2>`__ |
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443 implementation to handle most of the operations on the FM index. In |
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444 addition to spliced alignment, HISAT handles reads involving indels and |
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445 supports a paired-end alignment mode. Multiple processors can be used |
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446 simultaneously to achieve greater alignment speed. HISAT outputs |
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447 alignments in `SAM <http://samtools.sourceforge.net/SAM1.pdf>`__ format, |
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448 enabling interoperation with a large number of other tools (e.g. |
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449 `SAMtools <http://samtools.sourceforge.net>`__, |
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450 `GATK <http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit>`__) |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
|
451 that use SAM. HISAT is distributed under the `GPLv3 |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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changeset
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452 license <http://www.gnu.org/licenses/gpl-3.0.html>`__, and it runs on |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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453 the command line under Linux, Mac OS X and Windows. |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
|
454 |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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455 Running HISAT |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
|
456 ============= |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
|
457 |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
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458 Reporting |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
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459 --------- |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
|
460 |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
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461 The reporting mode governs how many alignments HISAT looks for, and how |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
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462 to report them. |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
|
463 |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
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464 In general, when we say that a read has an alignment, we mean that it |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
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465 has a `valid |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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466 alignment <#valid-alignments-meet-or-exceed-the-minimum-score-threshold>`__. |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
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467 When we say that a read has multiple alignments, we mean that it has |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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468 multiple alignments that are valid and distinct from one another. |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
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469 |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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470 Distinct alignments map a read to different places |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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471 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
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472 |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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473 Two alignments for the same individual read are "distinct" if they map |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
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474 the same read to different places. Specifically, we say that two |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
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475 alignments are distinct if there are no alignment positions where a |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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476 particular read offset is aligned opposite a particular reference offset |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
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477 in both alignments with the same orientation. E.g. if the first |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
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478 alignment is in the forward orientation and aligns the read character at |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
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479 read offset 10 to the reference character at chromosome 3, offset |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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480 3,445,245, and the second alignment is also in the forward orientation |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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481 and also aligns the read character at read offset 10 to the reference |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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482 character at chromosome 3, offset 3,445,245, they are not distinct |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
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483 alignments. |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
|
484 |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
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485 Two alignments for the same pair are distinct if either the mate 1s in |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
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486 the two paired-end alignments are distinct or the mate 2s in the two |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
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487 alignments are distinct or both. |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
|
488 |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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489 Default mode: search for one or more alignments, report each |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
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490 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
|
491 |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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492 HISAT searches for up to N distinct, primary alignments for each read, |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
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493 where N equals the integer specified with the ``-k`` parameter. Primary |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
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494 alignments mean alignments whose alignment score is equal or higher than |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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changeset
|
495 any other alignments. It is possible that multiple distinct alignments |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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changeset
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496 whave the same score. That is, if ``-k 2`` is specified, HISAT will |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
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497 search for at most 2 distinct alignments. The alignment score for a |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
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498 paired-end alignment equals the sum of the alignment scores of the |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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changeset
|
499 individual mates. Each reported read or pair alignment beyond the first |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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changeset
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500 has the SAM 'secondary' bit (which equals 256) set in its FLAGS field. |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
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501 See the `SAM specification <http://samtools.sourceforge.net/SAM1.pdf>`__ |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
|
502 for details. |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
|
503 |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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504 HISAT does not "find" alignments in any specific order, so for reads |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
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505 that have more than N distinct, valid alignments, HISAT does not |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
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506 gaurantee that the N alignments reported are the best possible in terms |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
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507 of alignment score. Still, this mode can be effective and fast in |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
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508 situations where the user cares more about whether a read aligns (or |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
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509 aligns a certain number of times) than where exactly it originated. |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
|
510 |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
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511 Alignment summmary |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
|
512 ------------------ |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
|
513 |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
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514 When HISAT finishes running, it prints messages summarizing what |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
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515 happened. These messages are printed to the "standard error" ("stderr") |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
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516 filehandle. For datasets consisting of unpaired reads, the summary might |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
|
517 look like this: |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
|
518 |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
|
519 :: |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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changeset
|
520 |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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diff
changeset
|
521 20000 reads; of these: |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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diff
changeset
|
522 20000 (100.00%) were unpaired; of these: |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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changeset
|
523 1247 (6.24%) aligned 0 times |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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changeset
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524 18739 (93.69%) aligned exactly 1 time |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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changeset
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525 14 (0.07%) aligned >1 times |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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changeset
|
526 93.77% overall alignment rate |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
527 |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
528 For datasets consisting of pairs, the summary might look like this: |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
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changeset
|
529 |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
530 :: |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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changeset
|
531 |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
532 10000 reads; of these: |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
533 10000 (100.00%) were paired; of these: |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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534 650 (6.50%) aligned concordantly 0 times |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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535 8823 (88.23%) aligned concordantly exactly 1 time |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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536 527 (5.27%) aligned concordantly >1 times |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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537 ---- |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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538 650 pairs aligned concordantly 0 times; of these: |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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539 34 (5.23%) aligned discordantly 1 time |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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540 ---- |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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541 616 pairs aligned 0 times concordantly or discordantly; of these: |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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542 1232 mates make up the pairs; of these: |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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543 660 (53.57%) aligned 0 times |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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544 571 (46.35%) aligned exactly 1 time |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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545 1 (0.08%) aligned >1 times |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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546 96.70% overall alignment rate |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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547 |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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548 The indentation indicates how subtotals relate to totals. |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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549 ]]> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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550 </help> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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551 <citations> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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552 <citation type="doi">10.1038/nmeth.3317</citation> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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553 </citations> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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554 </tool> |