| Next changeset 1:b7ea9a0e2714 (2014-06-14) |
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mgescan.xml |
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| diff -r 000000000000 -r c9fe27da991c mgescan.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mgescan.xml Sat Jun 14 19:04:23 2014 -0400 |
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| @@ -0,0 +1,101 @@ +<?xml version="1.0"?> + +<tool name="MGEScan" id="mgescan" version="0.0.1" workflow_compatible="false"> + <description> + MGEScan + </description> + <command interpreter="bash"> + mgescan.sh $input '$input.name' 3 $output $program $clade $qvalue_en $qvalue_rt $ltr_gff3 $nonltr_gff3 + <!-- mgescan.sh $input $input.name $hmmver $output $program $clade $qvalue_en $qvalue_rt $ltr_gff3 $nonltr_gff3 --> + </command> + <inputs> + <param format="txt" name="input" type="data" label="From"/> + <!--param name="hmmver" type="select" label="Hmmsearch version"> + <option selected="selected" value="3">3</option> + <option value="2">2</option> + </param--> + <param name="program" type="select" label="MGEScan"> + <option selected="selected" value="B">Both</option> + <option value="L">LTR</option> + <option value="N">nonLTR</option> + </param> + </inputs> + <outputs> + <data format="ltr.out" name="output"> + <filter>program != "N"</filter> + </data> + <data format="fasta" name="clade"> + <filter>program != "L"</filter> + </data> + <data format="qfile" name="qvalue_en"> + <filter>program != "L"</filter> + </data> + <data format="qfile" name="qvalue_rt"> + <filter>program != "L"</filter> + </data> + <data format="gff3" name="ltr_gff3"> + <filter>program != "N"</filter> + </data> + <data format="gff3" name="nonltr_gff3"> + <filter>program != "L"</filter> + </data> + + </outputs> + <help> +Running the program +=================== + +To run MGEScan, select input genome data in From select box, and select program either LTR, nonLTR or both. + +Click 'Execute' button. + +If you like to have more options to run LTR or nonLTR progrma, use separated tools on the left panel. +In LTR > MGEScan-LTR, preprocessing by repeatmasker and setting other variables are available e.g. distance(bp) between LTRs. + +Output +============ +A. MGEScan_LTR: +Upon completion, MGEScan-LTR generates a file "ltr.out". This output file has information +about clusters and coordinates of LTR retrotransposons identified. Each cluster of LTR +retrotransposons starts with the head line of "[cluster_number]---------", followed by +the information of LTR retrotransposons in the cluster. The columns for LTR +retrotransposons are as follows. + +1. LTR_id: unique id of LTRs identified. It consist of two components, sequence file name and id in the file. For example, chr1_2 is the second LTR retrotransposon in the chr1 file. +2. start position of 5’ LTR. +3. end position of 5’ LTR. +4. start position of 3’ LTR. +5. end position of 3’ LTR. +6. strand: + or -. +7. length of 5’ LTR. +8. length of 3’ LTR. +9. length of the LTR retrotransposon. +10. TSD on the left side of the LTR retotransposons. +11. TSD on the right side of the LTR retrotransposons. +12. di(tri)nucleotide on the left side of 5’LTR +13. di(tri)nucleotide on the right side of 5’LTR +14. di(tri)nucleotide on the left side of 3’LTR +15. di(tri)nucleotide on the right side of 3’LTR + +B. MGEScan_nonLTR: + Upon completion, MGEScan-nonLTR generates the directory, "info" in the data directory you + specified. In this "info" directory, two sub-directories ("full" and "validation") are + generated. + + - The "full" directory is for storing sequences of elements. Each subdirectory in "full" + is the name of clade. In each directory of clade, the DNA sequences of nonLTRs identified + are listed. Each sequence is in fasta format. The header contains the position + information of TEs identified: + [genome_file_name]_[start position in the sequence] + + For example, >chr1_333 means that this element start at 333bp in the "chr1" file. + + - The "validation" directory is for storing Q values. In the files "en" and "rt", the first column corresponds to the element name and the last column Q value. + +License +============ +Copyright 2014 Mina Rho, Haixu Tang. +You may redistribute this software under the terms of the GNU General Public License. + +</help> +</tool> |