Trinity_CTAT_galaxy/slncky.xml at master · cganote/Trinity_CTAT_galaxy · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
<tool id="slncky_pipeline" name="slncky_pipeline" version="0.0.1">

    <description>Running slncky</description>
    <command>
     #if str($bedfile) != "":
         python  $__tool_directory__/slncky_galaxy_wrapper.py --bedfile "$bedfile"
     #end if

     #if str($assembly) != "":
         --assembly "$assembly"
     #end if

     #if $min_overlap != "":
         --min_overlap "$min_overlap"
     #end if

     #if str($min_cluster) != "":
         --min_cluster "$min_cluster"
     #end if

     #if str($min_coding) != "":
         --min_coding "$min_coding"
     #end if

    #if str($minMatch) != "":
        --minMatch "$minMatch"
    #end if

    #if str($pad) != "":
        --pad "$pad"
    #end if

    #if str($gap_open) != "":
        --gap_open "$gap_open"
    #end if

    #if str($gap_extend) != "":
        --gap_extend "$gap_extend"
    #end if

    --web --html "$html_file" --html_files_path "$html_file.files_path"

    --can_lncs "$canonical_to_lncs" --clust_info "$cluster_info" --filt_info "$filtered_info"

    --lncs_bed "$lncs" --lncs_info "$lncs_info" --orfs "$orfs" --ortho_top "$orthologs_top" --ortho "$orthologs"

    </command>

    <inputs>
      <param name= "bedfile" format="bed" type="data" value="bedfile" label="Bed File:" help="Reconstructed transcripts (ex. from StringTie or Trinity)"/>
      <param name= "assembly" type="select" label="Assembly:" help="Reference Genome to be used">
             <option value="mm9">mm9</option>
             <option value="hg19">Hg19</option>
      </param>
      <param name="min_overlap" type="float" value="0.0" label="Min overlap" help="Remove any transcript that overlap annotated coding gene greater than min_overlap" />
      <param name="min_cluster" type="integer" value="2" label="Min cluster" help="Minimum size of duplication clusters to remove" />
      <param name="min_coding" type="float" value="0.1" label="Min exonic identity to filter out transcript that aligns to orthologous coding gene" help="default is set by learning coding alignment distribution from data"/>
      <param name="minMatch" type="float" value="0.1" label="Min match" help="Minimum match parameter for liftover" />
      <param name="pad" type="integer" value="0" label="Pad" help="No. of basepairs to search up- and down-stream when lifting over lnc to ortholog" />
      <param name="gap_open" type="text" value="200" label="Gap open penalty to pass to lastz" help="Decreasing this parameter will increase sensitivity of orthology search"/>
      <param name="gap_extend" type="text" value="40" label="Gap extend penalty to pass to lastz" help="Decreasing this parameter will increase sensitivity of orthology search."/>
    </inputs>

    <outputs>
           <data format="html" name="html_file" label="web_report"/>
           <data format="text" name="canonical_to_lncs" label="canonical_to_lncs" />
           <data format="text" name="cluster_info" label="cluster_info" />
           <data format="text" name="filtered_info" label="filtered_info" />
           <data format="bed" name="lncs" label="lncs" />
           <data format="text" name="lncs_info" label="lncs.info" />
           <data format="text" name="orfs" label="orfs" />
           <data format="text" name="orthologs_top" label="orthologs.top" />
           <data format="text" name="orthologs" label="orthologs" />
    </outputs>

    <stdio>
          <exit_code range="2"   level="fatal"   description="Out of Memory" />
          <exit_code range="3:5" level="warning" description="Low disk space" />
          <exit_code range="6:"  level="fatal"   description="Bad input dataset" />
          <exit_code range="99"  level="fatal"   description="Bad input dataset" />
    </stdio>
     <help>
.. class:: infomark

slncky is a tool for lncRNA discovery from RNA-Seq data. slncky filters a high-quality set of noncoding transcripts, discovers lncRNA orthologs, and characterizes conserved lncRNA evolution.

To learn more about slncky read their paper_ or visit their website_ .

.. _paper: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0880-9
.. _website: https://github.com/slncky/slncky

</help>
</tool>