Mercurial > repos > dfornika > tetyper

changeset 5:628c58844832 draft

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Uploaded
author dfornika
date Mon, 25 Nov 2019 23:59:52 +0000
parents ae8f5a2e723a
children 8fc05ce77eb7
files tetyper.xml
diffstat 1 files changed, 36 insertions(+), 28 deletions(-) [+]
line wrap: on
line diff
--- a/tetyper.xml	Sat Nov 23 04:19:45 2019 +0000
+++ b/tetyper.xml	Mon Nov 25 23:59:52 2019 +0000
@@ -14,6 +14,10 @@
             #end if
             --ref '${reference}'
             --flank_len '${flank_length}'
+            --min_reads '${min_reads}'
+            --min_each_strand '${min_each_strand}'
+            --min_mapped_len '${min_mapped_len}'
+            --min_qual '${min_qual}'
             --outprefix output
         ]]>
     </command>
@@ -32,7 +36,11 @@
             </when>
         </conditional>
         <param name="reference" type="data" format="fasta" label="Transposable Element Reference"/>
-        <param name="flank_length" type="integer" min="4" value="5" max="16" label="Flank Length"/>
+        <param name="flank_length" type="integer" min="4" value="5" max="16" label="Flank Length" help="Length of flanking region to extract."/>
+        <param name="min_reads" type="integer" min="1" value="10" max="100" label="Minimum Reads" help="Minimum read number for including a specific flanking sequence."/>
+        <param name="min_each_strand" type="integer" min="1" value="1" max="100" label="Minimum Reads (each strand)" help="Minimum read number for each strand for including a specific flanking sequence."/>
+        <param name="min_mapped_len" type="integer" min="8" value="30" max="100" label="Minimum Mapped Length" help="Minimum length of mapping for a read to be used in determining flanking sequences. Higher values are more robust to spurious mapping. Lower values will recover more reads."/>
+        <param name="min_qual" type="integer" min="0" value="10" max="100" label="Minimum quality" help="Minimum quality value across extracted flanking sequence." />
     </inputs>
     <outputs>
         <data name="summary" format="tabular" from_work_dir="output_summary.txt" label="${tool.name} on ${on_string}: summary"/>
@@ -50,33 +58,33 @@
 
 TETyper will produce a tab-seperated output file with the following outputs:
 
-+---------------+------------------------------------------------+
-|  Column       | Description                                    |
-+===============+================================================+
-|  Deletions    | A list of sequence ranges corresponding to regions of the reference classified as deletions for this sample, or "none" for no deletions. |
-+---------------+------------------------------------------------+
-|  Structural_variant     |                                      |
-+---------------+------------------------------------------------+
-|  SNPs_homozygous        |                                      |
-+---------------+------------------------------------------------+
-|  SNPs_heterozygous          |                                  |
-+---------------+------------------------------------------------+
-|  Heterozygous_SNP_counts         |                             |
-+---------------+------------------------------------------------+
-|  SNP_variant     |                                             |
-+---------------+------------------------------------------------+
-|  Combined_variant |                                            |
-+---------------+------------------------------------------------+
-|  Left_flanks         |                                         |
-+---------------+------------------------------------------------+
-|  Right_flanks    |                                             |
-+---------------+------------------------------------------------+
-|  Left_flank_counts    |                                        |
-+---------------+------------------------------------------------+
-|  Right_flank_counts     |                                      |
-+---------------+------------------------------------------------+
-|  X_Y_presence    |                                             |
-+---------------+------------------------------------------------+
++--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+
+|  Column                  | Description                                                                                                                              |
++==========================+==========================================================================================================================================+
+|  Deletions               | A list of sequence ranges corresponding to regions of the reference classified as deletions for this sample, or "none" for no deletions. |
++--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+
+|  Structural_variant      |                                                                                                                                          |
++--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+
+|  SNPs_homozygous         |                                                                                                                                          |
++--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+
+|  SNPs_heterozygous       |                                                                                                                                          |
++--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+
+|  Heterozygous_SNP_counts |                                                                                                                                          |
++--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+
+|  SNP_variant             |                                                                                                                                          |
++--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+
+|  Combined_variant        |                                                                                                                                          |
++--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+
+|  Left_flanks             |                                                                                                                                          |
++--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+
+|  Right_flanks            |                                                                                                                                          |
++--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+
+|  Left_flank_counts       |                                                                                                                                          |
++--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+
+|  Right_flank_counts      |                                                                                                                                          |
++--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+
+|  X_Y_presence            |                                                                                                                                          |
++--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+
 
       ]]>
     </help>