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ltr.xml |
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| diff -r b7ea9a0e2714 -r 2fd354a78c56 ltr.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ltr.xml Sat Jun 14 19:08:39 2014 -0400 |
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| @@ -0,0 +1,111 @@ +<?xml version="1.0"?> + +<tool name="MGEScan-LTR" id="mgescan-ltr" version="0.0.1" workflow_compatible="false"> + <description> + de novo identification of LTR retroelements + </description> + <!-- + <action module="galaxy.tools.actions.nonltr" class="nonltrToolAction"/> + <requirements> + <requirement type="package">HMMER</requirement> + <requirement type="package">EMBOSS</requirement> + </requirements> + --> + <command interpreter="bash"> + <!-- + /u/lee212/retrotminer/MGEScan_LTR/find_ltr.pl -genome=/u/lee212/retrotminer/MGEScan_nonLTR_v2/anoGam1/ + -data=/u/lee212/retrotminer/MGEScan_LTR/example/data/ -program=/u/lee212/retrotminer/MGEScan_LTR/ + --> + <!--mgescan.sh $input $input.name $hmmver $output L None None None $ltr_gff3 None--> + <!--mgescan.sh $input $input.name 3 $output L None None None $ltr_gff3 None--> + mgescan.sh $input $input.name 3 $output L None None None $ltr_gff3 None $sw_rm "$scaffold" $min_dist $max_dist $min_len_ltr $max_len_ltr $ltr_sim_condition $cluster_sim_condition $len_condition $repeatmasker + </command> + <inputs> + <!-- + <param name="genome" type="text" label="directory where input genome data exists" /> + <param name="data" type="text" label="directory of the output" /> + --> + <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--> + <!-- path.conf --> + <param name="sw_rm" type="select" display="checkboxes" multiple="True" label="enable repeatmasker, if necessary" help="Use this option if you are enable repeatmasker"> + <option value="Yes">Yes</option> + </param> + <param name="scaffold" type="text" label="path for the big file that has all scaffolds"/> + <!-- value.conf --> + <param name="min_dist" type="text" value="2000" label="minimum distance(bp) between LTRs" /> + <param name="max_dist" type="text" value="20000" label="maximum distance(bp) between LTRs" /> + <param name="min_len_ltr" type="text" value="130" label="minimum length(bp) of LTR"/> + <param name="max_len_ltr" type="text" value="2000" label="maximum length(bp) of LTR"/> + <param name="ltr_sim_condition" type="text" value="70" label="minimum similarity(%) for LTRs in an element"/> + <param name="cluster_sim_condition" type="text" value="70" label="inimum similarity(%) for LTRs in a cluster"/> + <param name="len_condition" type="text" value="70" label="minimum length(bp) for LTRs aligned in local alignment"/> + </inputs> + <outputs> + <data format="ltr.out" name="output" /> + <data format="gff3" name="ltr_gff3" /> + <data format="repeatmasker" name="repeatmasker" > + <filter>sw_rm == "Yes"</filter> + </data> + </outputs> + <help> +Running the program +=================== + +To run MGEScan-LTR, follow the steps below, + +1. Specify options that you like to have: + + * Check repeatmasker if you want to preprocess + * Check scaffold if the input file has all scaffolds. + +2. Update values: + + * min_dist: minimum distance(bp) between LTRs. + * max_dist: maximum distance(bp) between LTRS + * min_len_ltr: minimum length(bp) of LTR. + * max_len_ltr: maximum length(bp) of LTR. + * ltr_sim_condition: minimum similarity(%) for LTRs in an element. + * cluster_sim_condition: minimum similarity(%) for LTRs in a cluster + * len_condition: minimum length(bp) for LTRs aligned in local alignment. + +4. Click 'Execute' + + * mask known repeats other than LTR retrotransposons + * identify LTRs + +Output +====== + +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 5LTR +13. di(tri)nucleotide on the right side of 5LTR +14. di(tri)nucleotide on the left side of 3LTR +15. di(tri)nucleotide on the right side of 3LTR + +License +============ + +Copyright 2014 Mina Rho, Haixu Tang. +You may redistribute this software under the terms of the GNU General Public License. +</help> +</tool> |