Mercurial > repos > peterjc > seq_primer_clip
annotate tools/primers/seq_primer_clip.xml @ 3:f9ddb43ce28d draft
Uploaded v0.0.10a, fixes Biopython dependency setup
| author | peterjc |
|---|---|
| date | Fri, 13 Sep 2013 06:09:54 -0400 |
| parents | bd151574bbf3 |
| children |
| rev | line source |
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bd151574bbf3
Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
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1 <tool id="seq_primer_clip" name="Primer clip sequences" version="0.0.10"> |
| 0 | 2 <description>Trim off 5' or 3' primers</description> |
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bd151574bbf3
Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
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3 <requirements> |
| 3 | 4 <requirement type="package" version="1.61">biopython</requirement> |
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bd151574bbf3
Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
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5 <requirement type="python-module">Bio</requirement> |
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bd151574bbf3
Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
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6 </requirements> |
| 0 | 7 <version_command interpreter="python">seq_primer_clip.py --version</version_command> |
| 8 <command interpreter="python"> | |
| 9 seq_primer_clip.py $input_file $input_file.ext $primer_fasta $primer_type $mm $min_len $keep_negatives $output_file | |
| 10 </command> | |
| 11 <stdio> | |
| 12 <!-- Anything other than zero is an error --> | |
| 13 <exit_code range="1:" /> | |
| 14 <exit_code range=":-1" /> | |
| 15 </stdio> | |
| 16 <inputs> | |
| 17 <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file to clip" description="FASTA, FASTQ, or SFF format."/> | |
| 18 <param name="primer_fasta" type="data" format="fasta" label="FASTA file containing primer(s)"/> | |
| 19 <param name="primer_type" type="select" label="Type of primers"> | |
| 20 <option value="Forward">Forward (5') primers</option> | |
| 21 <option value="Reverse">Reverse (3') primers (given with respect to the forward strand)</option> | |
| 22 <option value="Reverse-complement">Reverse (3') primers (given with respect to the reverse strand)</option> | |
| 23 </param> | |
| 24 <param name="mm" type="integer" value="0" label="How many mismatches to allow? (0, 1 or 2)"> | |
| 25 <validator type="in_range" min="0" max="2" /> | |
| 26 </param> | |
| 27 <param name="keep_negatives" type="boolean" value="false" label="Keep reads with no matched primer"/> | |
| 28 <param name="min_len" type="integer" label="Minimum length for (clipped) sequences " value="1"/> | |
| 29 </inputs> | |
| 30 <outputs> | |
| 31 <data name="output_file" format="data" label="$primer_type primer clipped"> | |
| 32 <!-- TODO - Replace this with format="input:input_fastq" if/when that works --> | |
| 33 <change_format> | |
| 34 <when input_dataset="input_file" attribute="extension" value="sff" format="sff" /> | |
| 35 <when input_dataset="input_file" attribute="extension" value="fasta" format="fasta" /> | |
| 36 <when input_dataset="input_file" attribute="extension" value="fastq" format="fastq" /> | |
| 37 <when input_dataset="input_file" attribute="extension" value="fastqsanger" format="fastqsanger" /> | |
| 38 <when input_dataset="input_file" attribute="extension" value="fastqsolexa" format="fastqsolexa" /> | |
| 39 <when input_dataset="input_file" attribute="extension" value="fastqillumina" format="fastqillumina" /> | |
| 40 <when input_dataset="input_file" attribute="extension" value="fastqcssanger" format="fastqcssanger" /> | |
| 41 </change_format> | |
| 42 </data> | |
| 43 </outputs> | |
| 44 <tests> | |
| 45 <test> | |
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06e6112091aa
Uploaded v0.0.9, modifies tests to cope with current Tool Shed limitation.
peterjc
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46 <param name="input_file" value="MID4_GLZRM4E04_rnd30.fasta" ftype="fasta" /> |
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06e6112091aa
Uploaded v0.0.9, modifies tests to cope with current Tool Shed limitation.
peterjc
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47 <param name="primer_fasta" value="dop_primers.fasta" /> |
| 0 | 48 <param name="primer_type" value="Forward" /> |
| 49 <param name="mm" value="2" /> | |
| 50 <param name="keep_negatives" value="false" /> | |
| 51 <param name="min_len" value="35" /> | |
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06e6112091aa
Uploaded v0.0.9, modifies tests to cope with current Tool Shed limitation.
peterjc
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52 <output name="output_file" file="MID4_GLZRM4E04_rnd30_fclip.fasta" ftype="fasta" /> |
| 0 | 53 </test> |
| 54 <test> | |
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06e6112091aa
Uploaded v0.0.9, modifies tests to cope with current Tool Shed limitation.
peterjc
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changeset
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55 <param name="input_file" value="MID4_GLZRM4E04_rnd30.fastqsanger" ftype="fastqsanger" /> |
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06e6112091aa
Uploaded v0.0.9, modifies tests to cope with current Tool Shed limitation.
peterjc
parents:
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56 <param name="primer_fasta" value="dop_primers.fasta" /> |
| 0 | 57 <param name="primer_type" value="Forward" /> |
| 58 <param name="mm" value="2" /> | |
| 59 <param name="keep_negatives" value="false" /> | |
| 60 <param name="min_len" value="35" /> | |
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06e6112091aa
Uploaded v0.0.9, modifies tests to cope with current Tool Shed limitation.
peterjc
parents:
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diff
changeset
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61 <output name="output_file" file="MID4_GLZRM4E04_rnd30_fclip.fastqsanger" ftype="fastqsanger" /> |
| 0 | 62 </test> |
| 63 <test> | |
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06e6112091aa
Uploaded v0.0.9, modifies tests to cope with current Tool Shed limitation.
peterjc
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64 <param name="input_file" value="MID4_GLZRM4E04_rnd30.sff" ftype="sff" /> |
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06e6112091aa
Uploaded v0.0.9, modifies tests to cope with current Tool Shed limitation.
peterjc
parents:
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changeset
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65 <param name="primer_fasta" value="dop_primers.fasta" /> |
| 0 | 66 <param name="primer_type" value="Forward" /> |
| 67 <param name="mm" value="2" /> | |
| 68 <param name="keep_negatives" value="false" /> | |
| 69 <param name="min_len" value="35" /> | |
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06e6112091aa
Uploaded v0.0.9, modifies tests to cope with current Tool Shed limitation.
peterjc
parents:
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diff
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70 <output name="output_file" file="MID4_GLZRM4E04_rnd30_fclip.sff" ftype="sff" /> |
| 0 | 71 </test> |
| 72 <test> | |
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06e6112091aa
Uploaded v0.0.9, modifies tests to cope with current Tool Shed limitation.
peterjc
parents:
0
diff
changeset
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73 <param name="input_file" value="MID4_GLZRM4E04_rnd30_fclip.fasta" ftype="fasta" /> |
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06e6112091aa
Uploaded v0.0.9, modifies tests to cope with current Tool Shed limitation.
peterjc
parents:
0
diff
changeset
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74 <param name="primer_fasta" value="dop_primers.fasta" /> |
| 0 | 75 <param name="primer_type" value="Reverse" /> |
| 76 <param name="mm" value="2" /> | |
| 77 <param name="keep_negatives" value="true" /> | |
| 78 <param name="min_len" value="35" /> | |
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1
06e6112091aa
Uploaded v0.0.9, modifies tests to cope with current Tool Shed limitation.
peterjc
parents:
0
diff
changeset
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79 <output name="output_file" file="MID4_GLZRM4E04_rnd30_frclip.fasta" ftype="fasta" /> |
| 0 | 80 </test> |
| 81 <test> | |
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06e6112091aa
Uploaded v0.0.9, modifies tests to cope with current Tool Shed limitation.
peterjc
parents:
0
diff
changeset
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82 <param name="input_file" value="MID4_GLZRM4E04_rnd30_fclip.fastqsanger" ftype="fastqsanger" /> |
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06e6112091aa
Uploaded v0.0.9, modifies tests to cope with current Tool Shed limitation.
peterjc
parents:
0
diff
changeset
|
83 <param name="primer_fasta" value="dop_primers.fasta" /> |
| 0 | 84 <param name="primer_type" value="Reverse" /> |
| 85 <param name="mm" value="2" /> | |
| 86 <param name="keep_negatives" value="true" /> | |
| 87 <param name="min_len" value="35" /> | |
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1
06e6112091aa
Uploaded v0.0.9, modifies tests to cope with current Tool Shed limitation.
peterjc
parents:
0
diff
changeset
|
88 <output name="output_file" file="MID4_GLZRM4E04_rnd30_frclip.fastqsanger" ftype="fastqsanger" /> |
| 0 | 89 </test> |
| 90 <test> | |
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06e6112091aa
Uploaded v0.0.9, modifies tests to cope with current Tool Shed limitation.
peterjc
parents:
0
diff
changeset
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91 <param name="input_file" value="MID4_GLZRM4E04_rnd30_fclip.sff" ftype="sff" /> |
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06e6112091aa
Uploaded v0.0.9, modifies tests to cope with current Tool Shed limitation.
peterjc
parents:
0
diff
changeset
|
92 <param name="primer_fasta" value="dop_primers.fasta" /> |
| 0 | 93 <param name="primer_type" value="Reverse" /> |
| 94 <param name="mm" value="2" /> | |
| 95 <param name="keep_negatives" value="true" /> | |
| 96 <param name="min_len" value="35" /> | |
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1
06e6112091aa
Uploaded v0.0.9, modifies tests to cope with current Tool Shed limitation.
peterjc
parents:
0
diff
changeset
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97 <output name="output_file" file="MID4_GLZRM4E04_rnd30_frclip.sff" ftype="sff" /> |
| 0 | 98 </test> |
| 99 </tests> | |
| 100 <requirements> | |
| 101 <requirement type="python-module">Bio</requirement> | |
| 102 </requirements> | |
| 103 <help> | |
| 104 | |
| 105 **What it does** | |
| 106 | |
| 107 Looks for the given primer sequences (within the existing clipped sequence) and | |
| 108 further clips the reads to remove the primers and any preceding/trailing sequence. | |
| 109 | |
| 110 Reads containing a forward primer are reduced to just the sequence after (and | |
| 111 excluding) the forward primer. | |
| 112 | |
| 113 Reads containing a reverse primer are reduced to just the sequence before (and | |
| 114 excluding) the reverse primer. | |
| 115 | |
| 116 Degenerate primers can be specified using the standard IUPAC ambiguity codes, | |
| 117 thus a primer with an N would match A, C, T or G (or any of the IUPAC ambiguity | |
| 118 codes) and so on. | |
| 119 | |
| 120 Note that for SFF files only the clip/trim positions are edited - you will still | |
| 121 be able to extract the original full read (with any adapter sequence and poor | |
| 122 quality sequence) if you need to. | |
| 123 | |
| 124 .. class:: warningmark | |
| 125 | |
| 126 **Note**. This tool was initially written for Roche 454 data, and should also | |
| 127 work fine on Sanger or Ion Torrent as well. However, it is probably too slow | |
| 128 for use on large Illumina datasets. | |
| 129 | |
| 130 | |
| 131 **Citation** | |
| 132 | |
| 133 This tool uses Biopython. If you use this tool in scientific work leading to a | |
| 134 publication, please cite: | |
| 135 | |
| 136 Cock et al 2009. Biopython: freely available Python tools for computational | |
| 137 molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3. | |
| 138 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878. | |
| 139 | |
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2
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Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
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140 This tool is available to install into other Galaxy Instances via the Galaxy |
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bd151574bbf3
Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
1
diff
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141 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip |
| 0 | 142 </help> |
| 143 </tool> |