comparison pairwise.xml @ 11:ae65822c1fb7 draft default tip

planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1

10:cb5f2cc3dedc

**Outputs**

    - 'Pairwise' : the general output. It gives the information about what the tool has done for each pairwise.

    - 'Pairwise_DNA' : the output which contains nucleic sequences (of the pairwise) that are homologous. The sequences are with nucleotides. It shows for both the query and match :
        the name        
        the sequence in nucleotides

--------

**The AdaptSearch Pipeline**

 - IMPROVEMENT: Use conda dependencies for blast, samtools and python

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    </help>

    <expand macro="citations" />

</tool>

11:ae65822c1fb7

**Outputs**

    - 'Pairwise' : the general output. It gives the information about what the tool has done for each pairwise.

    - 'Pairwise_DNA' : the output which contains nucleic sequences (of the pairwise) that are homologous. The sequences are in nucleic format. There are one file per couple of species, and homologous pairs are written by sets of 4 lines : 

Exemple for two homologous pairs for the output file for species X/Y :

| >Gene_A_species_X_homologous_to_Gene_B_species_Y
| Nucleic_sequence_from_filter_assemblies
| >Gene_B_species_Y_homologous_to_Gene_A_species_X
| Nucleic_sequence_from_filter_assemblies
| >Gene_C_species_X_homologous_to_Gene_D_species_Y
| Nucleic_sequence_from_filter_assemblies
| >Gene_D_species_Y_homologous_to_Gene_C_species_X
| Nucleic_sequence_from_filter_assemblies


--------

**The AdaptSearch Pipeline**

 - IMPROVEMENT: Use conda dependencies for blast, samtools and python

    ]]>
    </help>

</tool>