comparison tools/protein_analysis/tmhmm2.xml @ 1:3ff1dcbb9440

Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository

0:bca9bc7fdaef

<tool id="tmhmm2" name="TMHMM 2.0" version="0.0.1">
    <description>Find transmembrane domains in protein sequences</description>
    <command interpreter="python">
      tmhmm2.py 8 $fasta_file $tabular_file
      ##I want the number of threads to be a Galaxy config option...
    </command>

        <requirement type="binary">tmhmm</requirement>
    </requirements>
    <tests>
        <test>
            <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta"/>
            <output name="tabular_file" file="four_human_proteins.tmhmm2.tsv" ftype="tabular"/>
        </test>
    </tests>
    <help>
    
**What it does**

 3. Expected number of amino acids in TM helices (ExpAA). If this number is larger than 18 it is very likely to be a transmembrane protein (OR have a signal peptide).
 4. Expected number of amino acids in TM helices in the first 60 amino acids of the protein (Exp60). If this number more than a few, be aware that a predicted transmembrane helix in the N-term could be a signal peptide.
 5. Number of transmembrane helices predicted by N-best.
 6. Topology predicted by N-best (encoded as a strip using o for output and i for inside)

Predicted TM segments in the n-terminal region sometime turn out to be signal peptides.

One of the most common mistakes by the program is to reverse the direction of proteins with one TM segment.

Do not use the program to predict whether a non-membrane protein is cytoplasmic or not. 

**Notes**

1:3ff1dcbb9440

<tool id="tmhmm2" name="TMHMM 2.0" version="0.0.3">
    <description>Find transmembrane domains in protein sequences</description>
    <command interpreter="python">
      tmhmm2.py 8 $fasta_file $tabular_file
      ##I want the number of threads to be a Galaxy config option...
    </command>

        <requirement type="binary">tmhmm</requirement>
    </requirements>
    <tests>
        <test>
            <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta"/>
            <output name="tabular_file" file="four_human_proteins.tmhmm2.tabular" ftype="tabular"/>
        </test>
        <test>
            <param name="fasta_file" value="empty.fasta" ftype="fasta"/>
            <output name="tabular_file" file="empty_tmhmm2.tabular" ftype="tabular"/>
        </test>
    </tests>
    <help>
    
**What it does**

 3. Expected number of amino acids in TM helices (ExpAA). If this number is larger than 18 it is very likely to be a transmembrane protein (OR have a signal peptide).
 4. Expected number of amino acids in TM helices in the first 60 amino acids of the protein (Exp60). If this number more than a few, be aware that a predicted transmembrane helix in the N-term could be a signal peptide.
 5. Number of transmembrane helices predicted by N-best.
 6. Topology predicted by N-best (encoded as a strip using o for output and i for inside)

Predicted TM segments in the n-terminal region sometimes turn out to be signal peptides.

One of the most common mistakes by the program is to reverse the direction of proteins with one TM segment (i.e. mixing up which end of the protein is outside and inside the membrane).

Do not use the program to predict whether a non-membrane protein is cytoplasmic or not. 

**Notes**