Mercurial > repos > iuc > hmmer_hmmsearch

comparison macros.xml @ 1:e779d71f871a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde
author iuc
date Mon, 14 Nov 2016 15:11:29 -0500
parents 1dde27bbdcba
children 284d40d6f5a1
comparison
equal deleted inserted replaced
0:1dde27bbdcba 1:e779d71f871a
389 <param name="w_beta" label="Tail mass at which window length is determined" 389 <param name="w_beta" label="Tail mass at which window length is determined"
390 help="(--w_beta)" optional="True" type="float"/> 390 help="(--w_beta)" optional="True" type="float"/>
391 <param name="w_length" label="Window Length" 391 <param name="w_length" label="Window Length"
392 help="(--w_length)" optional="True" type="integer" /> 392 help="(--w_length)" optional="True" type="integer" />
393 </xml> 393 </xml>
394 <token name="@INPUTHMMCHOICE@">
395 #if $input_hmm_conditional.input_hmm_source == "history":
396 '$input_hmm_conditional.hmmfile'
397 #else:
398 '$input_hmm_conditional.index.fields.db_path'
399 #end if
400 </token>
401 <xml name="input_hmm_choice">
402 <conditional name="input_hmm_conditional">
403 <param name="input_hmm_source" type="select" label="Use a built-in HMM model database or own from your history" >
404 <option value="indexed" selected="True">Use a built-in HMM model database</option>
405 <option value="history">Use a HMM database from history</option>
406 </param>
407 <when value="indexed">
408 <param name="index" type="select" label="Select a HMM model database" help="If your database of interest is not listed, contact the Galaxy administrator">
409 <options from_data_table="hmm_database">
410 <filter type="sort_by" column="2"/>
411 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
412 </options>
413 </param>
414 </when>
415 <when value="history">
416 <param name="hmmfile" type="data" label="HMM model" format="hmm2,hmm3"/>
417 </when> <!-- history -->
418 </conditional> <!-- input_hmm_conditional -->
419 </xml>
394 <xml name="input_hmm"> 420 <xml name="input_hmm">
395 <param name="hmmfile" type="data" label="HMM model" format="hmm2,hmm3"/> 421 <param name="hmmfile" type="data" label="HMM model" format="hmm2,hmm3"/>
396 </xml> 422 </xml>
397 <xml name="input_msa"> 423 <xml name="input_msa">
398 <param name="msafile" type="data" label="Multiple Sequence Alignment" format="stockholm,clustal,fasta" 424 <param name="msafile" type="data" label="Multiple Sequence Alignment" format="stockholm,clustal,fasta"
522 548
523 549
524 **Advanced Documentation** 550 **Advanced Documentation**
525 551
526 A more detailed look at the internals of the various filter pipelines was 552 A more detailed look at the internals of the various filter pipelines was
527 posted on the `developer's blog <http://selab.janelia.org/people/eddys/blog/?p=508>`__. 553 posted on the `developer's blog <https://cryptogenomicon.org/2011/09/19/hmmer3-is-stubborn/>`__.
528 The information posted there may be useful to those who are struggling with 554 The information posted there may be useful to those who are struggling with
529 poor-scoring sequences. 555 poor-scoring sequences.
530 556
531 ]]></token> 557 ]]></token>
532 <token name="@ADV_OPTS_HELP@"><![CDATA[ 558 <token name="@ADV_OPTS_HELP@"><![CDATA[
1039 <token name="@ATTRIBUTION@"><![CDATA[ 1065 <token name="@ATTRIBUTION@"><![CDATA[
1040 1066
1041 Attribution 1067 Attribution
1042 ----------- 1068 -----------
1043 1069
1044 This Galaxy tool relies on HMMER3_ from http://hmmer.janelia.org/ 1070 This Galaxy tool relies on HMMER3_
1045 Internally the software is cited as: 1071 Internally the software is cited as:
1046 1072
1047 :: 1073 ::
1048 1074
1049 # hmmscan :: search sequence(s) against a profile database 1075 # hmmscan :: search sequence(s) against a profile database
1054 1080
1055 The wrappers were written by Eric Rasche and is licensed under Apache2_. The 1081 The wrappers were written by Eric Rasche and is licensed under Apache2_. The
1056 documentation is copied from the HMMER3 documentation. 1082 documentation is copied from the HMMER3 documentation.
1057 1083
1058 .. _Apache2: http://www.apache.org/licenses/LICENSE-2.0 1084 .. _Apache2: http://www.apache.org/licenses/LICENSE-2.0
1059 .. _HMMER3: http://hmmer.janelia.org/ 1085 .. _HMMER3: http://hmmer.org/
1060 1086
1061 1087
1062 ]]></token> 1088 ]]></token>
1063 <token name="@HELP_PRE@"><![CDATA[ 1089 <token name="@HELP_PRE@"><![CDATA[
1064 1090