Mercurial > repos > bgruening > infernal
annotate cmstat.xml @ 14:2f8a8962ae22 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty
| author | bgruening |
|---|---|
| date | Fri, 04 Mar 2016 07:24:17 -0500 |
| parents | ffa96097e5b2 |
| children | 0ac29b4bb1cb |
| rev | line source |
|---|---|
| 12 | 1 <tool id="infernal_cmstat" name="Summary statistics" version="1.1.0.1"> |
| 9 | 2 <description>for covariance model (cmstat)</description> |
| 3 <requirements> | |
| 4 <requirement type="package">infernal</requirement> | |
| 12 | 5 <requirement type="package" version="1.1">infernal</requirement> |
| 13 | 6 <requirement type="package" version="8.22">gnu_coreutils</requirement> |
| 9 | 7 </requirements> |
| 8 <command> | |
| 13 | 9 <![CDATA[ |
| 9 | 10 ## a temp file is needed, because the standard tabular output from infernal is not usefull in Galaxy |
| 11 ## it will be converted to a tab delimited file and piped to Galaxy | |
| 12 temp_tabular_output=\$(mktemp); | |
| 13 | |
| 14 cmstat | |
| 15 | |
| 11 | 16 #if str($cm_opts.cm_opts_selector) == "db": |
| 9 | 17 $cm_opts.database.fields.path |
| 18 #else: | |
| 19 $cm_opts.cmfile | |
| 20 #end if | |
| 21 | |
| 22 > \$temp_tabular_output | |
| 23 ; | |
| 24 | |
| 25 ## 1. replace all lines starting # (comment lines) | |
| 26 ## 2. replace the first 18 spaces with tabs, 18th field is a free text field (can contain spaces) | |
| 27 sed -e 's/#.*$//' -e '/^$/d' -e 's/ /\t/g' -e 's/\t/ /18g' \$temp_tabular_output > $outfile | |
| 28 | |
| 13 | 29 ]]> |
| 9 | 30 </command> |
| 31 <inputs> | |
| 32 <conditional name="cm_opts"> | |
| 33 <param name="cm_opts_selector" type="select" label="Subject covariance models"> | |
| 34 <option value="db" selected="True">Locally installed covariance models</option> | |
| 35 <option value="histdb">Covariance model from your history</option> | |
| 36 </param> | |
| 37 <when value="db"> | |
| 38 <param name="database" type="select" label="Covariance models"> | |
| 39 <options from_file="infernal.loc"> | |
| 40 <column name="value" index="0"/> | |
| 41 <column name="name" index="1"/> | |
| 42 <column name="path" index="2"/> | |
| 43 </options> | |
| 44 </param> | |
| 45 </when> | |
| 46 <when value="histdb"> | |
| 47 <param name="cmfile" type="data" format="cm" label="Covariance models file from the history."/> | |
| 48 </when> | |
| 49 </conditional> | |
| 50 </inputs> | |
| 51 <outputs> | |
| 11 | 52 <data format="tabular" name="outfile" label="cmstat on ${on_string}"/> |
| 9 | 53 </outputs> |
| 54 <help> | |
| 13 | 55 <![CDATA[ |
| 9 | 56 |
| 57 | |
| 58 **What it does** | |
| 59 | |
| 60 The cmstat utility prints out a tabular file of summary statistics for each given covariance model. | |
| 61 | |
| 62 | |
|
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2f8a8962ae22
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty
bgruening
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63 **Output format** |
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2f8a8962ae22
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty
bgruening
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64 |
| 9 | 65 |
| 66 By default, cmstat prints general statistics of the model and the alignment it was built from, one line per model in a | |
| 13 | 67 tabular format. |
| 9 | 68 |
| 69 The columns are: | |
| 70 | |
| 71 (1) The index of this profile, numbering each on in the file starting from 1. | |
| 72 (2) The name of the profile. | |
| 73 (3) The optional accession of the profile, or ”-” if there is none. | |
| 74 (4) The number of sequences that the profile was estimated from. | |
| 75 (5) The effective number of sequences that the profile was estimated from, after Infernal applied an effective sequence number calculation such as the default entropy weighting. | |
| 76 (6) The length of the model in consensus residues (match states). | |
| 77 (7) The expected maximum length of a hit to the model. | |
| 78 (8) The number of basepairs in the model. | |
| 79 (9) The number of bifurcations in the model. | |
| 80 (10) What type of model will be used by default in cmsearch and cmscan for this profile, either ”cm” or ”hmm”. For profiles with 0 basepairs, this will be ”hmm” (unless the --nohmmonly option is used). For all other profiles, this will be ”cm”. | |
| 81 (11) Mean relative entropy per match state, in bits. This is the expected (mean) score per con- | |
| 82 sensus position. This is what the default entropy-weighting method for effective sequence | |
| 83 number estimation focuses on, so for default Infernal, this value will often reflect the default | |
| 84 target for entropy-weighting. If the ”model” field for this profile is ”hmm”, this field will be ”-”. | |
| 85 (12) Mean relative entropy per match state, in bits, if the CM were transformed into an HMM (information from structure is ignored). The larger the difference between the CM and HMM | |
| 86 relative entropy, the more the model will rely on structural conservation relative sequence conservation when identifying homologs. | |
| 87 | |
| 88 | |
|
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2f8a8962ae22
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty
bgruening
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89 For further questions please refere to the Infernal `Userguide <http://selab.janelia.org/software/infernal/Userguide.pdf>`_. |
| 9 | 90 |
| 13 | 91 ]]> |
| 9 | 92 </help> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty
bgruening
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93 <citations> |
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2f8a8962ae22
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty
bgruening
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94 <citation type="doi">10.1093/bioinformatics/btt509</citation> |
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2f8a8962ae22
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty
bgruening
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95 <citation type="bibtex"> |
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2f8a8962ae22
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty
bgruening
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96 @ARTICLE{bgruening_galaxytools, |
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2f8a8962ae22
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty
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97 Author = {Björn Grüning, Cameron Smith, Torsten Houwaart, Nicola Soranzo, Eric Rasche}, |
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2f8a8962ae22
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty
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98 keywords = {bioinformatics, ngs, galaxy, cheminformatics, rna}, |
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2f8a8962ae22
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty
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99 title = {{Galaxy Tools - A collection of bioinformatics and cheminformatics tools for the Galaxy environment}}, |
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2f8a8962ae22
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty
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100 url = {https://github.com/bgruening/galaxytools} |
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2f8a8962ae22
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty
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101 } |
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2f8a8962ae22
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty
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102 </citation> |
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2f8a8962ae22
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty
bgruening
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103 </citations> |
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2f8a8962ae22
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty
bgruening
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104 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty
bgruening
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105 |
| 9 | 106 </tool> |