Mercurial > repos > devteam > trimmer
annotate trimmer.xml @ 2:3983fbf107b6 draft default tip
planemo upload commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
| author | devteam |
|---|---|
| date | Fri, 09 Oct 2015 15:49:26 -0400 |
| parents | e632b6c79f7b |
| children |
| rev | line source |
|---|---|
| 0 | 1 <tool id="trimmer" name="Trim" version="0.0.1"> |
| 2 <description>leading or trailing characters</description> | |
| 3 <command interpreter="python"> | |
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e632b6c79f7b
Added quotes and brackets to appropriate command arguments
greg <greg@bx.psu.edu>
parents:
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diff
changeset
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4 trimmer.py -a -f "${input1}" -c "${col}" -s "${start}" -e "${end}" -i "${ignore}" "${fastq}" > "${out_file1}" |
| 0 | 5 </command> |
| 6 <inputs> | |
| 7 <param format="tabular,txt" name="input1" type="data" label="this dataset"/> | |
| 8 <param name="col" type="integer" value="0" label="Trim this column only" help="0 = process entire line" /> | |
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3983fbf107b6
planemo upload commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
devteam
parents:
1
diff
changeset
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9 <param name="start" type="integer" value="1" label="Trim from the beginning to this position" help="1 = do not trim the beginning"/> |
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3983fbf107b6
planemo upload commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
devteam
parents:
1
diff
changeset
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10 <param name="end" type="integer" value="0" label="Remove everything from this position to the end" help="0 = do not trim the end"/> |
| 0 | 11 <param name="fastq" type="select" label="Is input dataset in fastq format?" help="If set to YES, the tool will not trim evenly numbered lines (0, 2, 4, etc...)"> |
| 12 <option selected="true" value="">No</option> | |
| 13 <option value="-q">Yes</option> | |
| 14 </param> | |
| 15 <param name="ignore" type="select" display="checkboxes" multiple="True" label="Ignore lines beginning with these characters" help="lines beginning with these are not trimmed"> | |
| 16 <option value="62">></option> | |
| 17 <option value="64">@</option> | |
| 18 <option value="43">+</option> | |
| 19 <option value="60"><</option> | |
| 20 <option value="42">*</option> | |
| 21 <option value="45">-</option> | |
| 22 <option value="61">=</option> | |
| 23 <option value="124">|</option> | |
| 24 <option value="63">?</option> | |
| 25 <option value="36">$</option> | |
| 26 <option value="46">.</option> | |
| 27 <option value="58">:</option> | |
| 28 <option value="38">&</option> | |
| 29 <option value="37">%</option> | |
| 30 <option value="94">^</option> | |
| 31 <option value="35">#</option> | |
| 32 </param> | |
| 33 </inputs> | |
| 34 <outputs> | |
| 35 <data name="out_file1" format="input" metadata_source="input1"/> | |
| 36 </outputs> | |
| 37 <tests> | |
| 38 <test> | |
| 39 <param name="input1" value="trimmer_tab_delimited.dat"/> | |
| 40 <param name="col" value="0"/> | |
| 41 <param name="start" value="1"/> | |
| 42 <param name="end" value="13"/> | |
| 43 <param name="ignore" value="62"/> | |
| 44 <param name="fastq" value="No"/> | |
| 45 <output name="out_file1" file="trimmer_a_f_c0_s1_e13_i62.dat"/> | |
| 46 </test> | |
| 47 <test> | |
| 48 <param name="input1" value="trimmer_tab_delimited.dat"/> | |
| 49 <param name="col" value="2"/> | |
| 50 <param name="start" value="1"/> | |
| 51 <param name="end" value="2"/> | |
| 52 <param name="ignore" value="62"/> | |
| 53 <param name="fastq" value="No"/> | |
| 54 <output name="out_file1" file="trimmer_a_f_c2_s1_e2_i62.dat"/> | |
| 55 </test> | |
| 56 | |
| 57 </tests> | |
| 58 | |
| 59 <help> | |
| 60 | |
| 61 | |
| 62 **What it does** | |
| 63 | |
| 64 Trims specified number of characters from a dataset or its field (if dataset is tab-delimited). | |
| 65 | |
| 66 ----- | |
| 67 | |
| 68 **Example 1** | |
| 69 | |
| 70 Trimming this dataset:: | |
| 71 | |
| 72 1234567890 | |
| 73 abcdefghijk | |
| 74 | |
| 75 by setting **Trim from the beginning to this position** to *2* and **Remove everything from this position to the end** to *6* will produce:: | |
| 76 | |
| 77 23456 | |
| 78 bcdef | |
| 79 | |
| 80 ----- | |
| 81 | |
| 82 **Example 2** | |
| 83 | |
| 84 Trimming column 2 of this dataset:: | |
| 85 | |
| 86 abcde 12345 fghij 67890 | |
| 87 fghij 67890 abcde 12345 | |
| 88 | |
| 89 by setting **Trim content of this column only** to *2*, **Trim from the beginning to this position** to *2*, and **Remove everything from this position to the end** to *4* will produce:: | |
| 90 | |
| 91 abcde 234 fghij 67890 | |
| 92 fghij 789 abcde 12345 | |
| 93 | |
| 94 ----- | |
| 95 | |
| 96 **Trimming FASTQ datasets** | |
| 97 | |
| 98 This tool can be used to trim sequences and quality strings in fastq datasets. This is done by selected *Yes* from the **Is input dataset in fastq format?** dropdown. If set to *Yes*, the tool will skip all even numbered lines (see warning below). For example, trimming last 5 bases of this dataset:: | |
| 99 | |
| 100 @081017-and-081020:1:1:1715:1759 | |
| 101 GGACTCAGATAGTAATCCACGCTCCTTTAAAATATC | |
| 102 + | |
| 103 II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B | |
| 104 | |
| 105 cab done by setting **Remove everything from this position to the end** to 31:: | |
| 106 | |
| 107 @081017-and-081020:1:1:1715:1759 | |
| 108 GGACTCAGATAGTAATCCACGCTCCTTTAAA | |
| 109 + | |
| 110 II#IIIIIII$5+.(9IIIIIII$%*$G$A3 | |
| 111 | |
| 112 **Note** that headers are skipped. | |
| 113 | |
| 114 .. class:: warningmark | |
| 115 | |
| 116 **WARNING:** This tool will only work on properly formatted fastq datasets where (1) each read and quality string occupy one line and (2) '@' (read header) and "+" (quality header) lines are evenly numbered like in the above example. | |
| 117 | |
| 118 | |
| 119 </help> | |
| 120 </tool> |