Mercurial > repos > iuc > hisat2
annotate hisat2_macros.xml @ 30:6c19daec423d draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 591f9e8e46a9429bf28b64bae6f27f744bf08b3c"
author | iuc |
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date | Sun, 18 Jul 2021 17:50:55 +0000 |
parents | d4b55e2beb12 |
children | f4af63aaf57a |
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5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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1 <macros> |
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6c19daec423d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 591f9e8e46a9429bf28b64bae6f27f744bf08b3c"
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2 <token name="@TOOL_VERSION@">2.2.1</token> |
6c19daec423d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 591f9e8e46a9429bf28b64bae6f27f744bf08b3c"
iuc
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3 <token name="@VERSION_SUFFIX@">0</token> |
6c19daec423d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 591f9e8e46a9429bf28b64bae6f27f744bf08b3c"
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d5fe9aead222
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
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5 <xml name="paired_end_options"> |
d5fe9aead222
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
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6 |
d5fe9aead222
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
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7 <param name="rna_strandness" argument="--rna-strandness" type="select" label="Specify strand information" |
d5fe9aead222
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
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8 help="'FR' means a read corresponds to a transcript. 'RF' means a read corresponds to the reverse complemented counterpart of a transcript. With this option being used, every read alignment will have an XS attribute tag: '+' means a read belongs to a transcript on '+' strand of genome. '-' means a read belongs to a transcript on '-' strand of genome."> |
d5fe9aead222
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
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9 <option value="">Unstranded</option> |
d5fe9aead222
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
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10 <option value="FR">Forward (FR)</option> |
d5fe9aead222
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
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11 <option value="RF">Reverse (RF)</option> |
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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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12 </param> |
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d5fe9aead222
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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13 |
d5fe9aead222
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
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14 <conditional name="paired_options"> |
d5fe9aead222
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
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15 <param name="paired_options_selector" type="select" label="Paired-end options" help="See "Alignment Options" section of Help below for information"> |
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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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16 <option value="defaults">Use default values</option> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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17 <option value="advanced">Specify paired-end parameters</option> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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18 </param> |
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d5fe9aead222
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
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19 <when value="defaults"/> |
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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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20 <when value="advanced"> |
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d5fe9aead222
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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21 <param name="fr_rf_ff" argument="--fr/--rf/--ff" type="select" display="radio" label="Select the upstream/downstream mate orientations for a valid paired-end alignment against the forward reference strand" |
d5fe9aead222
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
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22 help="E.g., if `--fr` is specified and there is a candidate paired-end alignment where mate 1 appears upstream of the reverse complement of mate 2 and the fragment length constraints (`-I` and `-X`) are met, that alignment is valid. Also, if mate 2 appears upstream of the reverse complement of mate 1 and all other constraints are met, that too is valid. `--rf` likewise requires that an upstream mate1 be reverse-complemented and a downstream mate2 be forward-oriented. `--ff` requires both an upstream mate 1 and a downstream mate 2 to be forward-oriented; Default=--fr (appropriate for Illumina's Paired-end Sequencing Assay)"> |
d5fe9aead222
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
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23 <option value="--fr" selected="True">--fr</option> |
d5fe9aead222
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
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24 <option value="--rf">--rf</option> |
d5fe9aead222
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
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25 <option value="--ff">--ff</option> |
d5fe9aead222
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
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26 </param> |
d5fe9aead222
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
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27 <param argument="--no-mixed" name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="False" label="Disable no-mixed behavior" 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; default: False"/> |
d5fe9aead222
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
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28 <param argument="--no-discordant" name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="False" label="Disable no-discordant behavior" help="--no-discordant; 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 (`--fr`/`--rf`/`--ff`, `-I`, `-X`); default: False"/> |
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5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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29 </when> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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30 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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31 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
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32 </xml> |
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33 |
6ab42baa56e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d9ebd463afa1a41799aa53e9a68d0ea51093007e
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34 <xml name="dbKeyActions"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
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35 <conditional name="reference_genome.source"> |
0c16cad5e03b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
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36 <when value="indexed"> |
0c16cad5e03b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
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37 <action type="metadata" name="dbkey"> |
0c16cad5e03b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
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38 <option type="from_data_table" name="hisat2_indexes" column="1"> |
0c16cad5e03b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
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39 <filter type="param_value" ref="reference_genome.index" column="0"/> |
0c16cad5e03b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
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40 </option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
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41 </action> |
0c16cad5e03b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
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42 </when> |
0c16cad5e03b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
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43 <when value="history"> |
0c16cad5e03b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
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44 <action type="metadata" name="dbkey"> |
0c16cad5e03b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
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45 <option type="from_param" name="reference_genome.history_item" param_attribute="dbkey" /> |
0c16cad5e03b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
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46 </action> |
0c16cad5e03b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
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47 </when> |
0c16cad5e03b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
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48 </conditional> |
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49 </xml> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 0c0447365a23d4382b04745f22290608b47e5ff5"
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50 |
d4b55e2beb12
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 0c0447365a23d4382b04745f22290608b47e5ff5"
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51 <xml name= "nc_function" token_name="NO NAME GIVEN" token_argument="NO ARGUMENT GIVEN" token_label="NO LABEL GIVEN" token_help="" token_cselected="false" token_lselected="false" token_sselected="false" token_gselected="false"> |
d4b55e2beb12
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 0c0447365a23d4382b04745f22290608b47e5ff5"
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52 <param name="@NAME@" argument="@ARGUMENT@" type="select" display="radio" label="@LABEL@" help="@HELP@"> |
d4b55e2beb12
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 0c0447365a23d4382b04745f22290608b47e5ff5"
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53 <option value="C" selected="@CSELECTED@">Constant [f(x) = B]</option> |
d4b55e2beb12
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 0c0447365a23d4382b04745f22290608b47e5ff5"
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54 <option value="L" selected="@LSELECTED@">Linear [f(x) = B + A * x]</option> |
d4b55e2beb12
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 0c0447365a23d4382b04745f22290608b47e5ff5"
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55 <option value="S" selected="@SSELECTED@">Square root [f(x) = B + A * √x]</option> |
d4b55e2beb12
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 0c0447365a23d4382b04745f22290608b47e5ff5"
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56 <option value="G" selected="@GSELECTED@">Natural logarithm [f(x) = B + A * log(x)]</option> |
d4b55e2beb12
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 0c0447365a23d4382b04745f22290608b47e5ff5"
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57 </param> |
d4b55e2beb12
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 0c0447365a23d4382b04745f22290608b47e5ff5"
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58 </xml> |
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59 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
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60 </macros> |