Mercurial > repos > devteam > quality_filter
annotate quality_filter.xml @ 4:9deb51518bcc draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
| author | devteam |
|---|---|
| date | Wed, 11 Nov 2015 12:24:28 -0500 |
| parents | 6c6f15373f96 |
| children |
| rev | line source |
|---|---|
| 0 | 1 <tool id="qualityFilter" name="Filter nucleotides" version="1.0.1"> |
| 2 <description> based on quality scores</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.7.1">bx-python</requirement> | |
| 5 <requirement type="package" version="1.7.1">numpy</requirement> | |
| 6 </requirements> | |
| 7 <command interpreter="python"> | |
| 8 quality_filter.py | |
| 9 $input | |
| 10 $out_file1 | |
| 11 $primary_species | |
| 12 $mask_species | |
| 13 $score | |
| 14 $mask_char | |
| 15 ${mask_region.region} | |
| 16 #if $mask_region.region == "3" | |
| 17 ${mask_region.lengthr},${mask_region.lengthl} | |
| 18 #elif $mask_region.region == "0" | |
| 19 1 | |
| 20 #else | |
| 21 ${mask_region.length} | |
| 22 #end if | |
| 23 ${GALAXY_DATA_INDEX_DIR}/quality_scores.loc | |
| 24 </command> | |
| 25 <inputs> | |
| 26 <param format="maf" name="input" type="data" label="Select data"/> | |
| 27 <param name="primary_species" type="select" label="Use quality scores of" display="checkboxes" multiple="true"> | |
| 28 <options> | |
| 29 <filter type="data_meta" ref="input" key="species" /> | |
| 30 </options> | |
| 31 </param> | |
| 32 <param name="mask_species" type="select" label="Mask Species" display="checkboxes" multiple="true"> | |
| 33 <options> | |
| 34 <filter type="data_meta" ref="input" key="species" /> | |
| 35 </options> | |
| 36 </param> | |
|
4
9deb51518bcc
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
2
diff
changeset
|
37 <param name="score" type="integer" value="20" label="Quality score cut-off" help="Cut-off value of 20 means mask all nucleotides having quality score less than or equal to 20"/> |
|
9deb51518bcc
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
2
diff
changeset
|
38 <param name="mask_char" type="select" label="Mask character"> |
| 0 | 39 <option value="0" selected="true">#</option> |
| 40 <option value="1">$</option> | |
| 41 <option value="2">^</option> | |
| 42 <option value="3">*</option> | |
| 43 <option value="4">?</option> | |
| 44 <option value="5">N</option> | |
| 45 </param> | |
| 46 <conditional name="mask_region"> | |
| 47 <param name="region" type="select" label="Mask region"> | |
| 48 <option value="0" selected="true">Only the corresponding nucleotide </option> | |
| 49 <option value="1">Corresponding column + right-side neighbors</option> | |
| 50 <option value="2">Corresponding column + left-side neighbors</option> | |
| 51 <option value="3">Corresponding column + neighbors on both sides</option> | |
| 52 </param> | |
| 53 <when value="0"> | |
| 54 </when> | |
| 55 <when value="1"> | |
|
4
9deb51518bcc
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
2
diff
changeset
|
56 <param name="length" type="integer" value="2" label="Number of right-side neighbors"/> |
| 0 | 57 </when> |
| 58 <when value="2"> | |
|
4
9deb51518bcc
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
2
diff
changeset
|
59 <param name="length" type="integer" value="2" label="Number of left-side neighbors"/> |
| 0 | 60 </when> |
| 61 <when value="3"> | |
|
4
9deb51518bcc
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
2
diff
changeset
|
62 <param name="lengthr" type="integer" value="2" label="Number of neighbors on right-side" /> |
|
9deb51518bcc
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
2
diff
changeset
|
63 <param name="lengthl" type="integer" value="2" label="Number of neighbors on left-side" /> |
| 0 | 64 </when> |
| 65 </conditional> | |
| 66 </inputs> | |
| 67 <outputs> | |
| 68 <data format="maf" name="out_file1" metadata_source="input"/> | |
| 69 </outputs> | |
| 70 <requirements> | |
| 71 <requirement type="python-module">numpy</requirement> | |
| 72 </requirements> | |
| 73 <tests> | |
| 74 <test> | |
| 75 <param name="input" value="6.maf"/> | |
| 76 <param name="primary_species" value="panTro2"/> | |
| 77 <param name="mask_species" value="hg18"/> | |
| 78 <param name="score" value="50"/> | |
| 79 <param name="mask_char" value="0"/> | |
| 80 <param name="region" value="0" /> | |
| 81 <output name="out_file1" file="6_quality_filter.maf"/> | |
| 82 </test> | |
| 83 </tests> | |
| 84 <help> | |
| 85 | |
| 86 .. class:: infomark | |
| 87 | |
| 88 **What it does** | |
| 89 | |
| 90 This tool takes a MAF file as input and filters nucleotides in every alignment block of the MAF file based on their quality/PHRED scores. | |
| 91 | |
| 92 ----- | |
| 93 | |
| 94 .. class:: warningmark | |
| 95 | |
| 96 **Note** | |
| 97 | |
| 98 Any block/s not containing the primary species (species whose quality scores is to be used), will be omitted. | |
| 99 Also, any primary species whose quality scores are not available in Galaxy will be considered as a non-primary species. This info will appear as a message in the job history panel. | |
| 100 | |
| 101 ----- | |
| 102 | |
| 103 **Example** | |
| 104 | |
| 105 - For the following alignment block:: | |
| 106 | |
| 107 a score=4050.0 | |
| 108 s hg18.chrX 3719221 48 - 154913754 tattttacatttaaaataaatatgtaaatatatattttatatttaaaa | |
| 109 s panTro2.chrX 3560945 48 - 155361357 tattttatatttaaaataaagatgtaaatatatattttatatttaaaa | |
| 110 | |
| 111 - running this tool with **Primary species as panTro2**, **Mask species as hg18, panTro2**, **Quality cutoff as 20**, **Mask character as #** and **Mask region as only the corresponding position** will return:: | |
| 112 | |
| 113 a score=4050.0 | |
| 114 s hg18.chrX 3719221 48 - 154913754 ###tttac#####a###a#atatgtaaat###tattt#####ttaaaa | |
| 115 s panTro2.chrX 3560945 48 - 155361357 ###tttat#####a###a#agatgtaaat###tattt#####ttaaaa | |
| 116 | |
| 117 where, the positions containing # represent panTro2 nucleotides having quality scores less than 20. | |
| 118 </help> | |
| 119 </tool> |