mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-21 13:50:20 +08:00
Daniel Blankenberg
74784e1755
Biomart doesn't work on the trunk yet (Before or after this commit). axt to lav tool won't be functional until multiple datasets per history item is available on trunk - although I could make it so that only the lav file is generated and no fasta files, in which case it wouldn't be an issue.
130 lines
5.5 KiB
XML
130 lines
5.5 KiB
XML
<?xml version="1.0"?>
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<tool name="Upload File" id="upload1">
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<description>
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from your computer
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</description>
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<action module="galaxy.tools.actions.upload" class="UploadToolAction"/>
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<inputs>
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<param name="file_data" type="file" size="30" label="File"/>
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<param name="url_paste" type="text" area="true" size="5x35" label="URL/Text" help="Here you may specify a list of URLs (one per line) or paste the contents of a file."/>
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<param name="space_to_tab" type="select" display="checkboxes" multiple="True" label="Convert spaces to tabs" help="Use this option if you are entering intervals by hand.">
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<option value="Yes">Yes</option>
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</param>
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<param type="select" name="file_type" label="File Format" help="BED or Interval? See help below">
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<option value="auto" selected="yes">Auto-detect</option>
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<option value="bed">BED</option>
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<option value="interval">Genomic Intervals</option>
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<option value="fasta">FASTA</option>
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<option value="maf">Maf</option>
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<option value="axt">AXT</option>
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<option value="tabular">Tab delimited</option>
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<option value="gff">Gff</option>
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<option value="text">Other text type</option>
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</param>
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<param label="Genome" name="dbkey" type="select" dynamic_options="get_available_builds()"/>
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</inputs>
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<help>
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**Auto-detect**
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The system can detect FASTA, MAF, Wiggle, BED and Interval (BED with headers) formats. Other formats will be set to generic text files. If your file is not detected properly as one of the known formats it most likely means that it might have some format problems for example: different number of columns on different rows. You can still coerce the system to set your data to the format you think is should be (please send us a note if you see a case when a valid format is not detected).
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**BED**
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* Tab delimited format
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* Does not require header line
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* Contains 3 required fields:
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- chrom - The name of the chromosome (e.g. chr3, chrY, chr2_random) or contig (e.g. ctgY1).
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- chromStart - The starting position of the feature in the chromosome or contig. The first base in a chromosome is numbered 0.
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- chromEnd - The ending position of the feature in the chromosome or contig. The chromEnd base is not included in the display of the feature. For example, the first 100 bases of a chromosome are defined as chromStart=0, chromEnd=100, and span the bases numbered 0-99.
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* May contain 9 additional optional BED fields:
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- name - Defines the name of the BED line. This label is displayed to the left of the BED line in the Genome Browser window when the track is open to full display mode or directly to the left of the item in pack mode.
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- score - A score between 0 and 1000. If the track line useScore attribute is set to 1 for this annotation data set, the score value will determine the level of gray in which this feature is displayed (higher numbers = darker gray).
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- strand - Defines the strand - either '+' or '-'.
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- thickStart - The starting position at which the feature is drawn thickly (for example, the start codon in gene displays).
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- thickEnd - The ending position at which the feature is drawn thickly (for example, the stop codon in gene displays).
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- itemRgb - An RGB value of the form R,G,B (e.g. 255,0,0). If the track line itemRgb attribute is set to "On", this RBG value will determine the display color of the data contained in this BED line. NOTE: It is recommended that a simple color scheme (eight colors or less) be used with this attribute to avoid overwhelming the color resources of the Genome Browser and your Internet browser.
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- blockCount - The number of blocks (exons) in the BED line.
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- blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.
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- blockStarts - A comma-separated list of block starts. All of the blockStart positions should be calculated relative to chromStart. The number of items in this list should correspond to blockCount.
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* Example::
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chr22 1000 5000 cloneA 960 + 1000 5000 0 2 567,488, 0,3512
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chr22 2000 6000 cloneB 900 - 2000 6000 0 2 433,399, 0,3601
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Original description of the BED format can be found here_.
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.. _here: http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED
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-----
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**Genomic Intervals**
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- Tab delimited format
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- File must start with definition line in the following format (columns may be in any order).::
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#CHROM START END STRAND
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- CHROM - The name of the chromosome (e.g. chr3, chrY, chr2_random) or contig (e.g. ctgY1).
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- START - The starting position of the feature in the chromosome or contig. The first base in a chromosome is numbered 0.
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- END - The ending position of the feature in the chromosome or contig. The chromEnd base is not included in the display of the feature. For example, the first 100 bases of a chromosome are defined as chromStart=0, chromEnd=100, and span the bases numbered 0-99.
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- STRAND - Defines the strand - either '+' or '-'.
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- Example::
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#CHROM START END STRAND NAME COMMENT
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chr1 10 100 + exon myExon
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chrX 1000 10050 - gene myGene
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-----
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**FASTA**
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Fasta file may contain any number of sequences. Each sequence starts with a definition line identified by > symbol::
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>sequence1
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atgcgtttgcgtgc
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gtcggtttcgttgc
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>sequence2
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tttcgtgcgtatag
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tggcgcggtga
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-----
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**MAF**
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TBA and multiz multiple alignment format
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-----
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**AXT**
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blastz pairwise alignment format
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-----
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**Tab delimited**
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Any data in tab delimited format
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-----
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**Other text type**
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Any text file
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</help>
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<code file = "upload_code.py"/>
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</tool>
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