Mercurial > repos > iuc > hisat2
annotate hisat2.xml @ 14:526b91fbde60 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
author | iuc |
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date | Wed, 19 Jul 2017 04:57:27 -0400 |
parents | f4fa77189eb0 |
children | d5fe9aead222 |
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:
diff
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1 <?xml version="1.0"?> |
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f4fa77189eb0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 24fd129248023df91579027d9061468d01fc2350
iuc
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2 <tool id="hisat2" name="HISAT2" version="2.0.5.2" profile="17.01"> |
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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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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:
diff
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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:
diff
changeset
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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
changeset
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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:
diff
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7 <requirements> |
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2dbb7f0ea66f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 1baf0d1eb5d9cb012e4ce1385431461f26f7bc05
iuc
parents:
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8 <requirement type="package" version="2.0.5">hisat2</requirement> |
2dbb7f0ea66f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 1baf0d1eb5d9cb012e4ce1385431461f26f7bc05
iuc
parents:
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9 <requirement type="package" version="1.4">samtools</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:
diff
changeset
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10 </requirements> |
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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11 <stdio> |
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526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
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12 <regex level="fatal" match="hisat2-align exited with value 1" source="both" /> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
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13 <regex level="fatal" match="hisat2: not found" source="both" /> |
0
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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14 <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
changeset
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15 </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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16 <version_command>hisat2 --version</version_command> |
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4d0a3173cde0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 379063161020578e1bd306769116c1b691216b35
iuc
parents:
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17 <command><![CDATA[ |
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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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18 #if str($spliced_options.spliced_options_selector) == "advanced" and str($spliced_options.known_splice_gtf) != 'None': |
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2dbb7f0ea66f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 1baf0d1eb5d9cb012e4ce1385431461f26f7bc05
iuc
parents:
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19 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
parents:
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20 hisat2_extract_splice_sites.py splice_sites.gtf > splice_sites.txt && |
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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21 #end if |
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da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
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22 |
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
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23 @FASTQGZ_SETUP@ |
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
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24 |
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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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25 #if $reference_genome.reference_genome_source == "history": |
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2dbb7f0ea66f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 1baf0d1eb5d9cb012e4ce1385431461f26f7bc05
iuc
parents:
8
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26 ln -s '$reference_genome.history_item' genome.fa && |
2dbb7f0ea66f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 1baf0d1eb5d9cb012e4ce1385431461f26f7bc05
iuc
parents:
8
diff
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27 hisat2-build -p \${GALAXY_SLOTS:-1} genome.fa genome && |
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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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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:
diff
changeset
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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 = $reference_genome.index.fields.path |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
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31 #end if |
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2dbb7f0ea66f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 1baf0d1eb5d9cb012e4ce1385431461f26f7bc05
iuc
parents:
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32 hisat2 -p \${GALAXY_SLOTS:-1} -x '${index_path}' |
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526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
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33 #if str($input_format.paired.paired_selector) == 'paired': |
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da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
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34 -1 '${read1}' -2 '${read2}' |
0
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
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35 @paired_end_options@ |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
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36 #else: |
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da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
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37 -U '${read1}' |
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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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38 #if str( $input_format.paired.unaligned_file ) == "true": |
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da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
9
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39 #if $compressed == "GZ": |
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526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
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40 --un-gz '$output_unaligned_reads' |
10
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
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41 #else if $compressed == "BZ2": |
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526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
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42 --un-bz2 '$output_unaligned_reads' |
10
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
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43 #else: |
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526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
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44 --un '$output_unaligned_reads' |
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da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
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45 #end if |
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5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
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46 #end if |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
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47 #if str( $input_format.paired.aligned_file ) == "true": |
10
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
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48 #if $compressed == "GZ": |
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526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
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49 --al-gz '$output_aligned_reads' |
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da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
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50 #else if $compressed == "BZ2": |
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526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
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51 --al-bz2 '$output_aligned_reads' |
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da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
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52 #else: |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
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53 --al '$output_aligned_reads' |
10
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
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54 #end if |
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5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
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55 #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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56 #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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57 #if $input_format.input_format_selector == 'fasta': |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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58 -f |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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59 #end if |
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2dbb7f0ea66f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 1baf0d1eb5d9cb012e4ce1385431461f26f7bc05
iuc
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60 #if str($max_primary) |
0
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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61 -k ${max_primary} |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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62 #end if |
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2dbb7f0ea66f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 1baf0d1eb5d9cb012e4ce1385431461f26f7bc05
iuc
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63 #if str($max_seeds) |
2dbb7f0ea66f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 1baf0d1eb5d9cb012e4ce1385431461f26f7bc05
iuc
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64 --max-seeds $max_seeds |
2dbb7f0ea66f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 1baf0d1eb5d9cb012e4ce1385431461f26f7bc05
iuc
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65 #end if |
2dbb7f0ea66f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 1baf0d1eb5d9cb012e4ce1385431461f26f7bc05
iuc
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66 $secondary |
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5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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67 #if str($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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68 #if int( $input_options.skip ) > 0: |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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69 -s ${input_options.skip} |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
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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 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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72 -u ${input_options.stop_after} |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
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73 #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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74 -5 ${input_options.trim_five} -3 ${input_options.trim_three} |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
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75 #end if |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
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76 #if str($scoring_options.scoring_options_selector) == "advanced": |
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2dbb7f0ea66f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 1baf0d1eb5d9cb012e4ce1385431461f26f7bc05
iuc
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77 --ma ${scoring_options.match_bonus} |
0
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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78 --mp ${scoring_options.max_mismatch},${scoring_options.min_mismatch} |
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79 ${scoring_options.no_softclip} |
2dbb7f0ea66f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 1baf0d1eb5d9cb012e4ce1385431461f26f7bc05
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80 --np ${scoring_options.ambiguous_penalty} |
0
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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81 --rdg ${scoring_options.read_open_penalty},${scoring_options.read_extend_penalty} |
5bafe7d7a55e
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82 --rfg ${scoring_options.ref_open_penalty},${scoring_options.ref_extend_penalty} |
5bafe7d7a55e
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83 --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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84 --score-min ${scoring_options.function_type},${scoring_options.constant_term},${scoring_options.coefficient} |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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85 #end if |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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86 #if str($alignment_options.alignment_options_selector) == "advanced": |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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87 --n-ceil ${alignment_options.function_type},${alignment_options.constant_term},${alignment_options.coefficient} |
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88 ${alignment_options.ignore_quals} |
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89 ${alignment_options.skip_forward} |
f4fa77189eb0
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90 ${alignment_options.skip_reverse} |
0
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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91 #end if |
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92 #if str($spliced_options.spliced_options_selector) == "advanced": |
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93 --pen-cansplice ${spliced_options.canonical_penalty} |
f4fa77189eb0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 24fd129248023df91579027d9061468d01fc2350
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94 --pen-noncansplice ${spliced_options.noncanonical_penalty} |
0
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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95 --pen-canintronlen ${spliced_options.function_type},${spliced_options.constant_term},${spliced_options.coefficient} |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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96 --pen-noncanintronlen ${spliced_options.nc_function_type},${spliced_options.nc_constant_term},${spliced_options.nc_coefficient} |
5bafe7d7a55e
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97 #if str($spliced_options.known_splice_gtf) != 'None': |
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98 --known-splicesite-infile splice_sites.txt |
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99 #end if |
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100 ${spliced_options.no_spliced_alignment_options.no_spliced_alignment} |
2dbb7f0ea66f
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101 #if $spliced_options.no_spliced_alignment_options.no_spliced_alignment == '--no-spliced-alignment' |
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102 -I ${spliced_options.no_spliced_alignment_options.minins} |
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103 -X ${spliced_options.no_spliced_alignment_options.maxins} |
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104 #end if |
0
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105 --min-intronlen ${spliced_options.min_intron} |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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106 --max-intronlen ${spliced_options.max_intron} |
5bafe7d7a55e
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107 ${spliced_options.tma} |
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108 @strandedness_parameters@ |
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109 #end if |
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110 #if str($paired_options.paired_options_selector) == "advanced": |
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111 --minins ${paired_options.minins} --maxins ${paired_options.maxins} ${paired_options.no_mixed} ${paired_options.no_discordant} |
5bafe7d7a55e
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112 ${paired_options.dovetail} ${paired_options.contain} ${paired_options.overlap} |
5bafe7d7a55e
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113 #end if |
9
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114 | samtools sort - -@ \${GALAXY_SLOTS:-1} -l 6 -o '${output_alignments}' |
7
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115 ## Rename any output fastq files |
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116 #if $output_unaligned_reads_l and $output_unaligned_reads_r: |
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117 #set left = str($output_unaligned_reads_l).replace(".dat", ".1.dat") |
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118 #set right = str($output_unaligned_reads_l).replace(".dat", ".2.dat") |
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119 && mv '${left}' '${output_unaligned_reads_l}' |
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120 && mv '${right}' '${output_unaligned_reads_r}' |
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121 #end if |
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122 #if $output_aligned_reads_l and $output_aligned_reads_r: |
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123 #set left = str($output_aligned_reads_l).replace(".dat", ".1.dat") |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
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124 #set right = str($output_aligned_reads_l).replace(".dat", ".2.dat") |
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125 && mv '${left}' '${output_aligned_reads_l}' |
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126 && mv '${right}' '${output_aligned_reads_r}' |
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127 #end if |
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128 ]]></command> |
0
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129 <inputs> |
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130 <conditional name="input_format"> |
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131 <param name="input_format_selector" type="select" label="Input data format"> |
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132 <option value="fastq" selected="true">FASTQ</option> |
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133 <option value="fasta">FASTA</option> |
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134 </param> |
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135 <when value="fasta"> |
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136 <expand macro="paired_input_conditional" ftype="fasta" /> |
0
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137 </when> |
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138 <when value="fastq"> |
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139 <expand macro="paired_input_conditional" ftype="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" /> |
0
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140 </when> |
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141 </conditional> |
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142 <conditional name="reference_genome"> |
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143 <param name="reference_genome_source" type="select" label="Source for the reference genome to align against" help="Built-in references were created using default options"> |
14
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144 <option value="indexed" selected="true">Use a built-in genome</option> |
0
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145 <option value="history">Use a genome from history</option> |
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146 </param> |
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147 <when value="indexed"> |
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148 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> |
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149 <options from_data_table="hisat2_indexes"> |
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150 <filter type="sort_by" column="2" /> |
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151 <validator type="no_options" message="No genomes are available for the selected input dataset" /> |
0
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152 </options> |
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153 </param> |
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154 </when> |
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155 <when value="history"> |
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156 <param name="history_item" type="data" format="fasta" label="Select the reference genome" /> |
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157 </when> |
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158 </conditional> |
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159 <param name="max_primary" argument="-k" type="integer" optional="true" label="Primary alignments" 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. The alignment score for a paired-end alignment equals the sum of the alignment scores of the individual mates. Each reported read or pair alignment beyond the first has the SAM 'secondary' bit (which equals 256) set in its FLAGS field. For reads that have more than K distinct, valid alignments, hisat2 does not guarantee that the K alignments reported are the best possible in terms of alignment score. HISAT2 is not designed with large values for -k in mind, so when aligning reads to long repetitive genomes, a large K can be very, very slow. Default: 5 (HFM) or 10 (HGFM)" /> |
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160 <param name="max_seeds" argument="--max-seeds" type="integer" optional="true" label="Maximum number of seeds that will be extended" help="HISAT2, like other aligners, uses seed-and-extend approaches. HISAT2 tries to extend seeds to full-length alignments. HISAT2 extends up to these many seeds and skips the rest of the seeds. Large values for --max-seeds may improve alignment sensitivity, but HISAT2 is not designed with large values for --max-seeds in mind, and when aligning reads to long repetitive genomes, a large --max-seeds can be very, very slow. Default: 5 (HFM) or 10 (HGFM)" /> |
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161 <param argument="--secondary" type="boolean" truevalue="--secondary" falsevalue="" label="Report secondary alignments" /> |
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162 <conditional name="alignment_options"> |
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163 <param name="alignment_options_selector" type="select" label="Alignment options"> |
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164 <option value="defaults">Use default values</option> |
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165 <option value="advanced">Specify alignment parameters</option> |
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166 </param> |
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167 <when value="defaults" /> |
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168 <when value="advanced"> |
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169 <param name="function_type" argument="--n-ceil" type="select" display="radio" label="Function governing the maximum number of ambiguous characters (usually Ns and/or .s) allowed in a read as a function of read length" help="Reads exceeding this ceiling are filtered out"> |
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170 <option value="C">Constant [f(x) = B]</option> |
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171 <option value="L" selected="true">Linear [f(x) = B + A * x]</option> |
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172 <option value="S">Square root [f(x) = B + A * x²]</option> |
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173 <option value="G">Natural logarithm [f(x) = B + A * log(x)]</option> |
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174 </param> |
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175 <param name="constant_term" type="float" value="0" label="Constant term (B)" help="Constant term for the above function" /> |
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176 <param name="coefficient" type="float" value="0.15" label="Coefficient (A)" help="Coefficient for the above function" /> |
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177 <param argument="--ignore-quals" name="ignore_quals" type="boolean" truevalue="--ignore-quals" falsevalue="" label="Ignore quality values" 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" /> |
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178 <param argument="--nofw" name="skip_forward" type="boolean" truevalue="--nofw" falsevalue="" label="Skip forward strand of reference" help="If --nofw is specified, hisat2 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 hisat2 to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand" /> |
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179 <param argument="--norc" name="skip_reverse" type="boolean" truevalue="--norc" falsevalue="" label="Skip reverse strand of reference" help="If --norc is specified, hisat2 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 --norc causes hisat2 to explore only those paired-end configurations corresponding to fragments from the forward-complement (Watson) strand" /> |
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180 </when> |
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181 </conditional> |
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182 <conditional name="input_options"> |
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183 <param name="input_options_selector" type="select" label="Input options"> |
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184 <option value="defaults">Use default values</option> |
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185 <option value="advanced">Specify input parameters</option> |
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186 </param> |
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187 <when value="defaults" /> |
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188 <when value="advanced"> |
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189 <param name="skip" argument="-s" type="integer" min="0" value="0" label="Skip the first N reads or pairs in the input" /> |
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190 <param name="stop_after" argument="-u" type="integer" min="0" value="0" label="Stop after aligning N reads" help="Align the first N reads or read pairs from the input (after the first N reads or pairs have been skipped), then stop" /> |
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191 <param name="trim_five" argument="-5" type="integer" min="0" value="0" label="Trim 5' end" help="Trim N bases from 5' (left) end of each read before alignment" /> |
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192 <param name="trim_three" argument="-3" type="integer" min="0" value="0" label="Trim 3' end" help="Trim N bases from 3' (right) end of each read before alignment" /> |
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193 </when> |
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194 </conditional> |
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195 <conditional name="scoring_options"> |
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196 <param name="scoring_options_selector" type="select" label="Scoring options"> |
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197 <option value="defaults">Use default values</option> |
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198 <option value="advanced">Specify scoring parameters</option> |
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199 </param> |
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200 <when value="defaults" /> |
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201 <when value="advanced"> |
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202 <param name="function_type" argument="--score-min" type="select" display="radio" label="Function governing the minimum alignment score needed for an alignment to be considered "valid" (i.e. good enough to report)" help="This is a function of read length"> |
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203 <option value="C">Constant [f(x) = B]</option> |
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204 <option value="L" selected="true">Linear [f(x) = B + A * x]</option> |
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205 <option value="S">Square root [f(x) = B + A * x²]</option> |
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206 <option value="G">Natural logarithm [f(x) = B + A * log(x)]</option> |
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207 </param> |
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208 <param name="constant_term" type="float" value="0" label="Constant term (B)" help="Constant term for the above function" /> |
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209 <param name="coefficient" type="float" value="-0.2" label="Coefficient (A)" help="Coefficient for the above function" /> |
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210 <param argument="--ma" name="match_bonus" type="integer" value="2" label="Set match bonus" 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" /> |
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211 <param argument="--mp" name="max_mismatch" type="integer" value="6" label="Maximum mismatch penalty" 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" /> |
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212 <param argument="--mp" name="min_mismatch" type="integer" value="2" label="Minimum mismatch penalty" 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" /> |
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213 <param argument="--no-softclip" name="no_softclip" type="boolean" truevalue="--no-softclip" falsevalue="" label="Disallow soft-clipping" /> |
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214 <param argument="--np" name="ambiguous_penalty" type="integer" value="1" label="Ambiguous read penalty" help="Sets penalty for positions where the read, reference, or both, contain an ambiguous character such as N" /> |
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215 <param argument="--sp" name="soft_clip_penalty_max" type="integer" value="2" label="Maximum soft-clipping penalty" 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" /> |
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216 <param argument="--sp" name="soft_clip_penalty_min" type="integer" value="1" label="Minimum soft-clipping penalty" 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" /> |
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217 <param argument="--rdg" name="read_open_penalty" type="integer" value="5" label="Read gap open penalty" help="A read gap of length N gets a penalty of [open_penalty] + N * [extend_penalty]" /> |
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218 <param argument="--rdg" name="read_extend_penalty" type="integer" value="3" label="Read gap extend penalty" help="A read gap of length N gets a penalty of [open_penalty] + N * [extend_penalty]" /> |
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219 <param argument="--rfg" name="ref_open_penalty" type="integer" value="5" label="Reference gap open penalty" help="A reference gap of length N gets a penalty of [open_penalty] + N * [extend_penalty]" /> |
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220 <param argument="--rfg" name="ref_extend_penalty" type="integer" value="3" label="Reference gap extend penalty" help="A reference gap of length N gets a penalty of [open_penalty] + N * [extend_penalty]" /> |
0
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221 </when> |
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222 </conditional> |
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223 <conditional name="spliced_options"> |
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224 <param name="spliced_options_selector" type="select" label="Spliced alignment parameters"> |
0
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225 <option value="defaults">Use default values</option> |
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226 <option value="advanced">Specify spliced alignment parameters</option> |
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227 </param> |
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228 <when value="defaults" /> |
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229 <when value="advanced"> |
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230 <param name="canonical_penalty" argument="--pen-cansplice" type="integer" value="0" label="Penalty for canonical splice sites" /> |
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231 <param name="noncanonical_penalty" argument="--pen-noncansplice" type="integer" value="12" label="Penalty for non-canonical splice sites" /> |
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232 <param name="function_type" argument="--pen-canintronlen" type="select" display="radio" label="Penalty function for long introns with canonical splice sites" help="Alignments with shorter introns are preferred to those with longer ones"> |
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233 <option value="C">Constant [f(x) = B]</option> |
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234 <option value="L">Linear [f(x) = B + A * x]</option> |
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235 <option value="S">Square root [f(x) = B + A * x²]</option> |
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236 <option value="G" selected="true">Natural logarithm [f(x) = B + A * log(x)]</option> |
0
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237 </param> |
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238 <param name="constant_term" type="float" value="-8" label="Constant term (B)" help="Constant term for the above function" /> |
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239 <param name="coefficient" type="float" value="1" label="Coefficient (A)" help="Coefficient for the above function" /> |
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240 <param name="nc_function_type" argument="--pen-noncanintronlen" type="select" display="radio" label="Penalty function for long introns with non-canonical splice sites" help="Alignments with shorter introns are preferred to those with longer ones"> |
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241 <option value="C">Constant [f(x) = B]</option> |
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242 <option value="L">Linear [f(x) = B + A * x]</option> |
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243 <option value="S">Square root [f(x) = B + A * x²]</option> |
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244 <option value="G" selected="true">Natural logarithm [f(x) = B + A * log(x)]</option> |
0
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245 </param> |
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246 <param name="nc_constant_term" type="float" value="-8" label="Constant term (B)" help="Constant term for the above function" /> |
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247 <param name="nc_coefficient" type="float" value="1" label="Coefficient (A)" help="Coefficient for the above function" /> |
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248 <param name="min_intron" type="integer" value="20" label="Minimum intron length" /> |
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249 <param name="max_intron" type="integer" value="500000" label="Maximum intron length" /> |
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250 <param name="rna_strandness" argument="--rna-strandness" type="select" label="Specify strand-specific information" |
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251 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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252 <option value="">FR Unstranded</option> |
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253 <option value="R">First Strand (R/RF)</option> |
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254 <option value="F">Second Strand (F/FR)</option> |
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255 </param> |
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256 <conditional name="no_spliced_alignment_options"> |
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257 <param name="no_spliced_alignment" argument="--no-spliced-alignment" type="select" label="Disable spliced alignment"> |
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258 <option value="--no-spliced-alignment">True</option> |
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259 <option value="">False</option> |
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260 </param> |
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261 <when value="--no-spliced-alignment"> |
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262 <param name="minins" argument="-I" type="integer" value="0" label="Minimum fragment length for valid paired-end alignments" help="E.g. if -I 60 is specified and a paired-end alignment consists of two 20-bp alignments in the appropriate orientation with a 20-bp gap between them, that alignment is considered valid (as long as -X is also satisfied). A 19-bp gap would not be valid in that case. If trimming options -3 or -5 are also used, the -I constraint is applied with respect to the untrimmed mates. The larger the difference between -I and -X, the slower HISAT2 will run. This is because larger differences between -I and -X require that HISAT2 scan a larger window to determine if a concordant alignment exists. For typical fragment length ranges (200 to 400 nucleotides), HISAT2 is very efficient" /> |
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263 <param name="maxins" argument="-X" type="integer" value="500" label="Maximum fragment length for valid paired-end alignments" help="E.g. if -X 100 is specified and a paired-end alignment consists of two 20-bp alignments in the proper orientation with a 60-bp gap between them, that alignment is considered valid (as long as -I is also satisfied). A 61-bp gap would not be valid in that case. If trimming options -3 or -5 are also used, the -X constraint is applied with respect to the untrimmed mates, not the trimmed mates. The larger the difference between -I and -X, the slower HISAT2 will run. This is because larger differences between -I and -X require that HISAT2 scan a larger window to determine if a concordant alignment exists. For typical fragment length ranges (200 to 400 nucleotides), HISAT2 is very efficient" /> |
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264 </when> |
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265 <when value="" /> |
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266 </conditional> |
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267 <param name="known_splice_gtf" type="data" format="gtf" optional="true" label="GTF file with known splice sites" /> |
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268 <param name="tma" type="select" display="radio" label="Transcriptome assembly reporting"> |
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269 <option value="">Use default reporting.</option> |
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270 <option value="--tmo">Report only those alignments within known transcripts.</option> |
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271 <option value="--dta">Report alignments tailored for transcript assemblers including StringTie.</option> |
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272 <option value="--dta-cufflinks">Report alignments tailored specifically for Cufflinks.</option> |
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273 </param> |
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274 </when> |
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275 </conditional> |
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276 <conditional name="paired_options"> |
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277 <param name="paired_options_selector" type="select" label="Paired alignment parameters"> |
0
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278 <option value="defaults">Use default values</option> |
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279 <option value="advanced">Specify paired alignment parameters</option> |
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280 </param> |
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281 <when value="defaults" /> |
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282 <when value="advanced"> |
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283 <param argument="--minins" type="integer" value="0" label="Minimum fragment length" help="The minimum fragment length for valid paired-end alignments. 0 sets no minimum" /> |
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284 <param argument="--maxins" type="integer" value="500" label="Maximum fragment length" help="The maximum fragment length for valid paired-end alignments" /> |
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285 <param name="no_mixed" argument="--no-mixed" type="boolean" truevalue="--no-mixed" falsevalue="" label="Disable finding alignments for individual mates" |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
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286 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" /> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
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287 <param name="no_discordant" argument="--no-discordant" type="boolean" truevalue="--no-discordant" falsevalue="" label="Disable looking for discordant alignments" |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
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288 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" /> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
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289 <param argument="--dovetail" type="boolean" truevalue="--dovetail" falsevalue="" label="Mates not dovetail" 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" /> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
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290 <param name="contain" argument="--no-contain" type="boolean" truevalue="--no-contain" falsevalue="" label="Mates cannot contain others" help="If one mate alignment contains the other, consider that to be non-concordant" /> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
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291 <param name="overlap" argument="--no-overlap" type="boolean" truevalue="--no-overlap" falsevalue="" label="Mates cannot overlap" help="If one mate alignment overlaps the other at all, consider that to be non-concordant" /> |
0
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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292 </when> |
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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293 </conditional> |
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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294 </inputs> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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295 <outputs> |
9
2dbb7f0ea66f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 1baf0d1eb5d9cb012e4ce1385431461f26f7bc05
iuc
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296 <data name="output_alignments" format="bam"> |
3
b1e25f9b5eab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 9a9d44116b21d9a155b5cc274475e78c14915059
iuc
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297 <actions> |
9
2dbb7f0ea66f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 1baf0d1eb5d9cb012e4ce1385431461f26f7bc05
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298 <conditional name="reference_genome.reference_genome_source"> |
2dbb7f0ea66f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 1baf0d1eb5d9cb012e4ce1385431461f26f7bc05
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299 <when value="indexed"> |
2dbb7f0ea66f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 1baf0d1eb5d9cb012e4ce1385431461f26f7bc05
iuc
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300 <action type="metadata" name="dbkey"> |
2dbb7f0ea66f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 1baf0d1eb5d9cb012e4ce1385431461f26f7bc05
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301 <option type="from_data_table" name="hisat2_indexes" column="1" offset="0"> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
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302 <filter type="param_value" column="0" compare="startswith" value="#" keep="false" /> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
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303 <filter type="param_value" ref="reference_genome.index" column="0" /> |
9
2dbb7f0ea66f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 1baf0d1eb5d9cb012e4ce1385431461f26f7bc05
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304 </option> |
2dbb7f0ea66f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 1baf0d1eb5d9cb012e4ce1385431461f26f7bc05
iuc
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changeset
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305 </action> |
2dbb7f0ea66f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 1baf0d1eb5d9cb012e4ce1385431461f26f7bc05
iuc
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changeset
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306 </when> |
2dbb7f0ea66f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 1baf0d1eb5d9cb012e4ce1385431461f26f7bc05
iuc
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307 <when value="history"> |
2dbb7f0ea66f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 1baf0d1eb5d9cb012e4ce1385431461f26f7bc05
iuc
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changeset
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308 <action type="metadata" name="dbkey"> |
2dbb7f0ea66f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 1baf0d1eb5d9cb012e4ce1385431461f26f7bc05
iuc
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309 <option type="from_param" name="reference_genome.history_item" param_attribute="dbkey" /> |
2dbb7f0ea66f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 1baf0d1eb5d9cb012e4ce1385431461f26f7bc05
iuc
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changeset
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310 </action> |
2dbb7f0ea66f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 1baf0d1eb5d9cb012e4ce1385431461f26f7bc05
iuc
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311 </when> |
2dbb7f0ea66f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 1baf0d1eb5d9cb012e4ce1385431461f26f7bc05
iuc
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312 </conditional> |
3
b1e25f9b5eab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 9a9d44116b21d9a155b5cc274475e78c14915059
iuc
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313 </actions> |
b1e25f9b5eab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 9a9d44116b21d9a155b5cc274475e78c14915059
iuc
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314 </data> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
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315 <data name="output_unaligned_reads" format="fastqsanger" label="${tool.name} on ${on_string}: unaligned reads"> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
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316 <filter>input_format['paired']['unaligned_file'] is True and input_format['paired']['paired_selector'] == 'single'</filter> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
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317 <actions> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
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318 <action type="format"> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
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319 <option type="from_param" name="input_format.paired.reads" param_attribute="ext" /> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
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320 </action> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
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321 </actions> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
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322 </data> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
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diff
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323 <data name="output_aligned_reads" format="fastqsanger" label="${tool.name} on ${on_string}: aligned reads"> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
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324 <filter>input_format['paired']['aligned_file'] is True and input_format['paired']['paired_selector'] == 'single'</filter> |
7
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
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325 <actions> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
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changeset
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326 <action type="format"> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
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327 <option type="from_param" name="input_format.paired.reads" param_attribute="ext" /> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
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328 </action> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
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329 </actions> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
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330 </data> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
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331 <data name="output_unaligned_reads_l" format="fastqsanger" label="${tool.name} on ${on_string}: unaligned reads (L)"> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
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332 <filter>input_format['paired']['unaligned_file'] is True and input_format['paired']['paired_selector'] == 'paired'</filter> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
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changeset
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333 <actions> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
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334 <conditional name="input_format.paired.collection.collection_selector"> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
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335 <when value="collection"> |
7
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
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336 <action type="format"> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
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337 <option type="from_param" name="input_format.paired.collection.reads.forward" param_attribute="ext" /> |
7
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
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changeset
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338 </action> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
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339 </when> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
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340 <when value="files"> |
7
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
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341 <action type="format"> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
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342 <option type="from_param" name="input_format.paired.collection.forward" param_attribute="ext" /> |
7
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
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343 </action> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
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344 </when> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
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345 </conditional> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
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346 </actions> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
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347 </data> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
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348 <data name="output_unaligned_reads_r" format="fastqsanger" label="${tool.name} on ${on_string}: unaligned reads (R)"> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
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349 <filter>input_format['paired']['unaligned_file'] is True and input_format['paired']['paired_selector'] == 'paired'</filter> |
7
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
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changeset
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350 <actions> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
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351 <conditional name="input_format.paired.collection.collection_selector"> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
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352 <when value="collection"> |
7
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
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changeset
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353 <action type="format"> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
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354 <option type="from_param" name="input_format.paired.collection.reads.reverse" param_attribute="ext" /> |
7
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
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changeset
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355 </action> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
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changeset
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356 </when> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
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changeset
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357 <when value="files"> |
7
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
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changeset
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358 <action type="format"> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
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diff
changeset
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359 <option type="from_param" name="input_format.paired.collection.reverse" param_attribute="ext" /> |
7
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
360 </action> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
361 </when> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
362 </conditional> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
363 </actions> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
364 </data> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
365 <data name="output_aligned_reads_l" format="fastqsanger" label="${tool.name} on ${on_string}: aligned reads (L)"> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
366 <filter>input_format['paired']['aligned_file'] is True and input_format['paired']['paired_selector'] == 'paired'</filter> |
7
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
367 <actions> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
368 <conditional name="input_format.paired.collection.collection_selector"> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
369 <when value="collection"> |
7
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
370 <action type="format"> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
371 <option type="from_param" name="input_format.paired.collection.reads.forward" param_attribute="ext" /> |
7
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
372 </action> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
373 </when> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
374 <when value="files"> |
7
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
375 <action type="format"> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
376 <option type="from_param" name="input_format.paired.collection.forward" param_attribute="ext" /> |
7
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
377 </action> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
378 </when> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
379 </conditional> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
380 </actions> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
381 </data> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
382 <data name="output_aligned_reads_r" format="fastqsanger" label="${tool.name} on ${on_string}: aligned reads (R)"> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
383 <filter>input_format['paired']['aligned_file'] is True and input_format['paired']['paired_selector'] == 'paired'</filter> |
7
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
384 <actions> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
385 <conditional name="input_format.paired.collection.collection_selector"> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
386 <when value="collection"> |
7
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
387 <action type="format"> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
388 <option type="from_param" name="input_format.paired.collection.reads.reverse" param_attribute="ext" /> |
7
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
389 </action> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
390 </when> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
391 <when value="files"> |
7
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
392 <action type="format"> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
393 <option type="from_param" name="input_format.paired.collection.reverse" param_attribute="ext" /> |
7
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
394 </action> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
395 </when> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
396 </conditional> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
397 </actions> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
398 </data> |
0
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
399 </outputs> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
400 <tests> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
401 <test> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
402 <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
|
403 <param name="paired_selector" value="paired" /> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
404 <param name="collection_selector" value="files" /> |
0
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
405 <param name="reference_genome_source" value="history" /> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
406 <param name="history_item" ftype="fasta" value="phiX.fa" /> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
407 <param name="forward" ftype="fastqsanger" value="hisat_input_1_forward.fastq" /> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
408 <param name="reverse" ftype="fastqsanger" value="hisat_input_1_reverse.fastq" /> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
409 <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" 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
|
410 </test> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
411 <test> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
412 <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
|
413 <param name="paired_selector" value="paired" /> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
414 <param name="collection_selector" value="files" /> |
0
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
415 <param name="reference_genome_source" value="history" /> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
416 <param name="history_item" ftype="fasta" value="phiX.fa" /> |
0
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
417 <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
|
418 <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
|
419 <param name="trim_five" value="15" /> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
420 <param name="forward" ftype="fastqsanger" value="hisat_input_2_forward.fastq" /> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
421 <param name="reverse" ftype="fastqsanger" value="hisat_input_2_reverse.fastq" /> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
422 <output name="output_alignments" file="hisat_output_2.bam" ftype="bam" 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
|
423 </test> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
424 <test> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
425 <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
|
426 <param name="paired_selector" value="paired" /> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
427 <param name="collection_selector" value="files" /> |
0
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
428 <param name="reference_genome_source" value="history" /> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
429 <param name="history_item" ftype="fasta" value="phiX.fa" /> |
0
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
430 <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
|
431 <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
|
432 <param name="trim_five" value="15" /> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
433 <param name="forward" ftype="fastqsanger" value="hisat_input_2_forward.fastq" /> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
434 <param name="reverse" ftype="fastqsanger" value="hisat_input_2_reverse.fastq" /> |
0
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
435 <param name="paired_end_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
|
436 <param name="no_mixed" value="True" /> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
437 <param name="no_discordant" value="True" /> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
438 <output name="output_alignments" file="hisat_output_3.bam" ftype="bam" 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
|
439 </test> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
440 <test> |
7
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
441 <param name="input_format_selector" value="fasta" /> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
442 <param name="paired_selector" value="single" /> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
443 <param name="reference_genome_source" value="history" /> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
444 <param name="history_item" ftype="fasta" value="phiX.fa" /> |
7
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
445 <param name="unaligned_file" value="true" /> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
446 <param name="aligned_file" value="true" /> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
447 <param name="reference_genome_source" value="history" /> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
448 <param name="history_item" ftype="fasta" value="phiX.fa" /> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
449 <param name="reads" ftype="fasta" value="test_unaligned_reads.fasta" /> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
450 <output name="output_unaligned_reads" file="test_unaligned_reads.fasta" /> |
7
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
451 </test> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
452 <test> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
453 <param name="input_format_selector" value="fasta" /> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
454 <param name="paired_selector" value="paired" /> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
455 <param name="collection_selector" value="files" /> |
7
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
456 <param name="reference_genome_source" value="history" /> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
457 <param name="history_item" ftype="fasta" value="phiX.fa" /> |
7
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
458 <param name="unaligned_file" value="true" /> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
459 <param name="aligned_file" value="true" /> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
460 <param name="reference_genome_source" value="history" /> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
461 <param name="history_item" ftype="fasta" value="phiX.fa" /> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
462 <param name="forward" ftype="fasta" value="test_unaligned_reads.fasta" /> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
463 <param name="reverse" ftype="fasta" value="test_unaligned_reads.fasta" /> |
7
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
464 <output name="output_unaligned_reads_l" file="test_unaligned_reads.fasta" /> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
465 <output name="output_unaligned_reads_r" file="test_unaligned_reads.fasta" /> |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
6
diff
changeset
|
466 </test> |
10
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
9
diff
changeset
|
467 <test><!-- Ensure fastqsanger.gz works --> |
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
9
diff
changeset
|
468 <param name="input_format_selector" value="fastq" /> |
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
9
diff
changeset
|
469 <param name="paired_selector" value="paired" /> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
470 <param name="collection_selector" value="files" /> |
10
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
9
diff
changeset
|
471 <param name="reference_genome_source" value="history" /> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
472 <param name="history_item" ftype="fasta" value="phiX.fa" /> |
10
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
9
diff
changeset
|
473 <param name="input_options_selector" value="advanced" /> |
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
9
diff
changeset
|
474 <param name="trim_three" value="15" /> |
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
9
diff
changeset
|
475 <param name="trim_five" value="15" /> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
476 <param name="forward" ftype="fastqsanger.gz" value="hisat_input_2_forward.fastq.gz" /> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
477 <param name="reverse" ftype="fastqsanger.gz" value="hisat_input_2_reverse.fastq.gz" /> |
10
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
9
diff
changeset
|
478 <param name="paired_end_options_selector" value="advanced" /> |
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
9
diff
changeset
|
479 <param name="no_mixed" value="True" /> |
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
9
diff
changeset
|
480 <param name="no_discordant" value="True" /> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
481 <output name="output_alignments" file="hisat_output_3.bam" ftype="bam" lines_diff="2" /> |
10
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
9
diff
changeset
|
482 </test> |
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
9
diff
changeset
|
483 <test><!-- Ensure fastqsanger.bz2 works --> |
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
9
diff
changeset
|
484 <param name="input_format_selector" value="fastq" /> |
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
9
diff
changeset
|
485 <param name="paired_selector" value="paired" /> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
486 <param name="collection_selector" value="files" /> |
10
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
9
diff
changeset
|
487 <param name="reference_genome_source" value="history" /> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
488 <param name="history_item" ftype="fasta" value="phiX.fa" /> |
10
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
9
diff
changeset
|
489 <param name="input_options_selector" value="advanced" /> |
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
9
diff
changeset
|
490 <param name="trim_three" value="15" /> |
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
9
diff
changeset
|
491 <param name="trim_five" value="15" /> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
492 <param name="forward" ftype="fastqsanger.bz2" value="hisat_input_2_forward.fastq.bz2" /> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
493 <param name="reverse" ftype="fastqsanger.bz2" value="hisat_input_2_reverse.fastq.bz2" /> |
10
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
9
diff
changeset
|
494 <param name="paired_end_options_selector" value="advanced" /> |
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
9
diff
changeset
|
495 <param name="no_mixed" value="True" /> |
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
9
diff
changeset
|
496 <param name="no_discordant" value="True" /> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
497 <output name="output_alignments" file="hisat_output_3.bam" ftype="bam" lines_diff="2" /> |
10
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
9
diff
changeset
|
498 </test> |
0
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
499 </tests> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
500 <help><![CDATA[ |
0
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
501 Introduction |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
502 ============ |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
503 |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
504 What is HISAT? |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
505 -------------- |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
506 |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
507 `HISAT <http://ccb.jhu.edu/software/hisat>`__ is a fast and sensitive |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
508 spliced alignment program. As part of HISAT, we have developed a new |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
509 indexing scheme based on the Burrows-Wheeler transform |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
510 (`BWT <http://en.wikipedia.org/wiki/Burrows-Wheeler_transform>`__) and |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
511 the `FM index <http://en.wikipedia.org/wiki/FM-index>`__, called |
5bafe7d7a55e
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512 hierarchical indexing, that employs two types of indexes: (1) one global |
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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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513 FM index representing the whole genome, and (2) many separate local FM |
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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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514 indexes for small regions collectively covering the genome. Our |
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515 hierarchical index for the human genome (about 3 billion bp) includes |
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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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516 ~48,000 local FM indexes, each representing a genomic region of |
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517 ~64,000bp. As the basis for non-gapped alignment, the FM index is |
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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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518 extremely fast with a low memory footprint, as demonstrated by |
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519 `Bowtie <http://bowtie-bio.sf.net>`__. In addition, HISAT provides |
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520 several alignment strategies specifically designed for mapping different |
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521 types of RNA-seq reads. All these together, HISAT enables extremely fast |
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522 and sensitive alignment of reads, in particular those spanning two exons |
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523 or more. As a result, HISAT is much faster >50 times than |
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524 `TopHat2 <http://ccb.jhu.edu/software/tophat>`__ with better alignment |
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525 quality. Although it uses a large number of indexes, the memory |
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526 requirement of HISAT is still modest, approximately 4.3 GB for human. |
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527 HISAT uses the `Bowtie2 <http://bowtie-bio.sf.net/bowtie2>`__ |
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528 implementation to handle most of the operations on the FM index. In |
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529 addition to spliced alignment, HISAT handles reads involving indels and |
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530 supports a paired-end alignment mode. Multiple processors can be used |
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531 simultaneously to achieve greater alignment speed. HISAT outputs |
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532 alignments in `SAM <http://samtools.sourceforge.net/SAM1.pdf>`__ format, |
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533 enabling interoperation with a large number of other tools (e.g. |
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534 `SAMtools <http://samtools.sourceforge.net>`__, |
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535 `GATK <http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit>`__) |
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536 that use SAM. HISAT is distributed under the `GPLv3 |
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537 license <http://www.gnu.org/licenses/gpl-3.0.html>`__, and it runs on |
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538 the command line under Linux, Mac OS X and Windows. |
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539 |
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540 Running HISAT |
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541 ============= |
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542 |
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543 Reporting |
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544 --------- |
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545 |
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546 The reporting mode governs how many alignments HISAT looks for, and how |
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547 to report them. |
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548 |
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549 In general, when we say that a read has an alignment, we mean that it |
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550 has a `valid |
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551 alignment <#valid-alignments-meet-or-exceed-the-minimum-score-threshold>`__. |
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552 When we say that a read has multiple alignments, we mean that it has |
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553 multiple alignments that are valid and distinct from one another. |
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554 |
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555 Distinct alignments map a read to different places |
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556 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ |
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557 |
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558 Two alignments for the same individual read are "distinct" if they map |
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559 the same read to different places. Specifically, we say that two |
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560 alignments are distinct if there are no alignment positions where a |
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561 particular read offset is aligned opposite a particular reference offset |
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562 in both alignments with the same orientation. E.g. if the first |
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563 alignment is in the forward orientation and aligns the read character at |
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564 read offset 10 to the reference character at chromosome 3, offset |
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565 3,445,245, and the second alignment is also in the forward orientation |
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566 and also aligns the read character at read offset 10 to the reference |
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567 character at chromosome 3, offset 3,445,245, they are not distinct |
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568 alignments. |
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569 |
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570 Two alignments for the same pair are distinct if either the mate 1s in |
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571 the two paired-end alignments are distinct or the mate 2s in the two |
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572 alignments are distinct or both. |
5bafe7d7a55e
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573 |
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574 Default mode: search for one or more alignments, report each |
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575 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ |
5bafe7d7a55e
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576 |
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577 HISAT searches for up to N distinct, primary alignments for each read, |
5bafe7d7a55e
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578 where N equals the integer specified with the ``-k`` parameter. Primary |
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579 alignments mean alignments whose alignment score is equal or higher than |
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580 any other alignments. It is possible that multiple distinct alignments |
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581 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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582 search for at most 2 distinct alignments. The alignment score for a |
5bafe7d7a55e
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583 paired-end alignment equals the sum of the alignment scores of the |
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changeset
|
584 individual mates. Each reported read or pair alignment beyond the first |
5bafe7d7a55e
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iuc
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585 has the SAM 'secondary' bit (which equals 256) set in its FLAGS field. |
5bafe7d7a55e
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586 See the `SAM specification <http://samtools.sourceforge.net/SAM1.pdf>`__ |
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587 for details. |
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|
588 |
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589 HISAT does not "find" alignments in any specific order, so for reads |
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|
590 that have more than N distinct, valid alignments, HISAT does not |
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|
591 gaurantee that the N alignments reported are the best possible in terms |
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592 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
iuc
parents:
diff
changeset
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593 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
iuc
parents:
diff
changeset
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594 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
iuc
parents:
diff
changeset
|
595 |
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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596 Alignment summmary |
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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597 ------------------ |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
598 |
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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599 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
iuc
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changeset
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600 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
iuc
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diff
changeset
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601 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
iuc
parents:
diff
changeset
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602 look like this: |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
603 |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
604 :: |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
605 |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
606 20000 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
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607 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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diff
changeset
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608 1247 (6.24%) 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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diff
changeset
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609 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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diff
changeset
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610 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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diff
changeset
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611 93.77% 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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diff
changeset
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612 |
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
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613 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
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diff
changeset
|
614 |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
615 :: |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
616 |
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
|
617 10000 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
|
618 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
iuc
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diff
changeset
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619 650 (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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diff
changeset
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620 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
parents:
diff
changeset
|
621 527 (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
parents:
diff
changeset
|
622 ---- |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
623 650 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
parents:
diff
changeset
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624 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
parents:
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changeset
|
625 ---- |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
626 616 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
parents:
diff
changeset
|
627 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
parents:
diff
changeset
|
628 660 (53.57%) aligned 0 times |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
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629 571 (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
parents:
diff
changeset
|
630 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
parents:
diff
changeset
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631 96.70% 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
|
632 |
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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633 The indentation indicates how subtotals relate to totals. |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
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diff
changeset
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634 ]]></help> |
0
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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635 <citations> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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636 <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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changeset
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637 </citations> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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638 </tool> |