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add more parameters to macros
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@shiltemann
shiltemann committed Dec 17, 2024
1 parent f9a5c90 commit dac2590
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Showing 3 changed files with 39 additions and 34 deletions.
22 changes: 5 additions & 17 deletions tools/emboss_5/emboss_needle.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -27,24 +27,12 @@ needle -asequence '$asequence'
<inputs>
<param argument="-asequence" type="data" format="fasta" label="Sequence 1" />
<param argument="-bsequence" type="data" format="fasta" label="Sequence 2" />

<expand macro="scoring_matrix"/>
<param argument="-gapopen" type="float" value="10.0" min="1.0" max="100.0" label="Gap open penalty" />
<param argument="-gapextend" type="float" value="0.5" min="0.0" max="10.0" label="Gap extension penalty" />
<conditional name="endgap">
<param argument="-endweight" type="select" label="Apply end gap penalties?" help="">
<option value="yes">yes</option>
<option value="no" selected="true">no</option>
</param>
<when value="yes">
<param argument="-endopen" type="float" value="10.0" min="0.0" max="100.0" label="Penalty for creation of and end gap." help="The best value depends on the choice of comparison matrix. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences."/>
<param argument="-endextend" type="float" value="0.5" min="0.0" max="10.0" label="The end gap extensionpenalty" help="this penalty is added to the end gap penalty for each base or residue in the end gap."/>
</when>
<when value="no"/>
</conditional>
<param argument="-brief" type="select" label="Brief identity and similarity">
<option value="yes">Yes</option>
<option value="no">No</option>
</param>
<expand macro="gap_penalties"/>
<expand macro="endgap_penalties"/>
<expand macro="param_brief"/>

<expand macro="choose_alignment_output_format"/>
</inputs>
<outputs>
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23 changes: 6 additions & 17 deletions tools/emboss_5/emboss_needleall.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -29,25 +29,14 @@ needleall
<inputs>
<param argument="-asequence" type="data" format="fasta" label="Sequence set 1" />
<param argument="-bsequence" type="data" format="fasta" label="Sequence seet 2" />

<expand macro="scoring_matrix"/>
<param argument="-gapopen" type="float" value="10.0" min="1.0" max="100.0" label="Gap open penalty" />
<param argument="-gapextend" type="float" value="0.5" min="0.0" max="10.0" label="Gap extension penalty" />
<conditional name="endgap">
<param argument="-endweight" type="select" label="Apply end gap penalties?" help="">
<option value="yes">yes</option>
<option value="no" selected="true">no</option>
</param>
<when value="yes">
<param argument="-endopen" type="float" value="10.0" min="0.0" max="100.0" label="Penalty for creation of and end gap." help="The best value depends on the choice of comparison matrix. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences."/>
<param argument="-endextend" type="float" value="0.5" min="0.0" max="10.0" label="The end gap extensionpenalty" help="this penalty is added to the end gap penalty for each base or residue in the end gap."/>
</when>
<when value="no"/>
</conditional>
<expand macro="gap_penalties"/>
<expand macro="endgap_penalties"/>
<expand macro="param_brief"/>

<param argument="-minscore" type="float" value="1.0" min="-10.0" max="100.0" label="Minimum alignment score to report an alignment." help=""/>
<param argument="-brief" type="select" label="Brief identity and similarity">
<option value="yes">Yes</option>
<option value="no">No</option>
</param>

<expand macro="choose_alignment_output_format"/>
</inputs>
<outputs>
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28 changes: 28 additions & 0 deletions tools/emboss_5/macros.xml
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Expand Up @@ -133,6 +133,34 @@
<option value="SSSUB">SSSUB</option>
</param>
</xml>

<xml name="param_brief">
<param argument="-brief" type="select" label="Brief identity and similarity">
<option value="yes">Yes</option>
<option value="no">No</option>
</param>
</xml>

<xml name="gap_penalties">
<param argument="-gapopen" type="float" value="10.0" min="1.0" max="100.0" label="Gap open penalty" />
<param argument="-gapextend" type="float" value="0.5" min="0.0" max="10.0" label="Gap extension penalty" />
</xml>

<xml name="endgap_penalties">
<conditional name="endgap">
<param argument="-endweight" type="select" label="Apply end gap penalties?" help="">
<option value="yes">yes</option>
<option value="no" selected="true">no</option>
</param>
<when value="yes">
<param argument="-endopen" type="float" value="10.0" min="0.0" max="100.0" label="Penalty for creation of and end gap." help="The best value depends on the choice of comparison matrix. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences."/>
<param argument="-endextend" type="float" value="0.5" min="0.0" max="10.0" label="The end gap extensionpenalty" help="this penalty is added to the end gap penalty for each base or residue in the end gap."/>
</when>
<when value="no"/>
</conditional>

</xml>

<xml name="choose_alignment_output_format">
<param name="out_format1" type="select" label="Output alignment file format">
<option value="srspair">SRS pair (p)</option>
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