| Previous changeset 10:ac8a12ac883c (2021-11-17) Next changeset 12:b88bee4ff652 (2022-03-24) |
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Commit message:
"planemo upload commit 1d7e9e2b3b84912e176c84013dca70b962edc43f" |
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modified:
coast_report.xml macros.xml |
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| diff -r ac8a12ac883c -r ccd8cae6e3aa coast_report.xml --- a/coast_report.xml Wed Nov 17 14:18:37 2021 +0000 +++ b/coast_report.xml Thu Mar 24 11:14:02 2022 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="coast_report" name="COAST - Report generator" version="0.2.0"> +<tool id="coast_report" name="COAST - Report" version="0.2.1"> <description>Recreate the report and outputs with different settings</description> <macros> <import>macros.xml</import> @@ -47,7 +47,7 @@ <param name="min_cov" value="30" /> <param name="min_id" value="30" /> <param name="hypothetical" value="true" /> -<!-- <output name="coast_report" file="report_h/coast_report.html" lines_diff="4"/>--> + <output name="coast_report" file="report_h/coast_report.html" lines_diff="4"/> <output name="bh_results" file="report_h/bh_results.tab" /> <output name="coast_results" file="report_h/coast_results.tab" /> </test> |
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| diff -r ac8a12ac883c -r ccd8cae6e3aa macros.xml --- a/macros.xml Wed Nov 17 14:18:37 2021 +0000 +++ b/macros.xml Thu Mar 24 11:14:02 2022 +0000 |
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| @@ -1,7 +1,7 @@ <macros> - <token name="@TOOL_VERSION@">0.2.0</token> + <token name="@TOOL_VERSION@">0.2.1</token> <xml name="requirements"> - <requirement type="package" version="0.2.0">coast</requirement> + <requirement type="package" version="0.2.1">coast</requirement> </xml> <xml name="citations_coast"> <citation type="bibtex">@misc{noauthor_coast_nodate, @@ -127,7 +127,7 @@ <param name="outfmt" type="select" optional="true" multiple="true" display="checkboxes" label="Select outputs"> <option value="b" selected="true">Best-hits tabular file</option> <option value="a" selected="true">Results tabular file</option> -<!-- <option value="r" selected="true">Summarized Report</option>--> + <option value="r" selected="true">Summarized Report</option> </param> </xml> <token name="@OUTPUT_FORMAT@"><![CDATA[ @@ -143,13 +143,13 @@ ]]></token> <xml name="aai_filter"> - <param name="aai" type="integer" value="10" label="AAIc filtering score"> + <param name="aai" type="integer" value="10" label="TAAI filtering score"> <validator type="in_range" min="0" max="100" message="Value not in the permitted range. Only values from O to 100 allowed."/> </param> - <param name="min_cov" type="integer" value="50" label="Minimum Coverage for AAIbd hit selection"> + <param name="min_cov" type="integer" value="50" label="Minimum Coverage for AAI hit selection"> <validator type="in_range" min="0" max="100" message="Value not in the permitted range. Only values from O to 100 allowed."/> </param> - <param name="min_id" type="integer" value="40" label="Minimum Amino Acid Identity for AAIbd hit selection"> + <param name="min_id" type="integer" value="40" label="Minimum Amino Acid Identity for AAI hit selection"> <validator type="in_range" min="0" max="100" message="Value not in the permitted range. Only values from O to 100 allowed."/> </param> </xml> @@ -222,20 +222,20 @@ <option value="taxonlist_pre_defined">Pre-defined taxonomic filters</option> <option value="taxonlist">Comma separated list</option> </param> - <when value="taxonlist_pre_defined"> - <param name="taxonlist" type="select" optional="true" label="Select pre-defined taxonomic filters"> - <option value="10239">Viruses - 10239</option> - <option value="2157">Archaea - 2157</option> - <option value="2">Bacteria - 2</option> - </param> - </when> - <when value="taxonlist"> - <param name="taxonlist" type="text" optional="true" label="Comma separated list of TAXIDs nodes, ranking species or lower"/> - </when> + <when value="taxonlist_pre_defined"> + <param name="taxonlist" type="select" optional="true" label="Select pre-defined taxonomic filters"> + <option value="10239">Viruses - 10239</option> + <option value="2157">Archaea - 2157</option> + <option value="2">Bacteria - 2</option> + </param> + </when> + <when value="taxonlist"> + <param name="taxonlist" type="text" optional="true" label="Comma separated list of TAXIDs nodes, ranking species or lower"/> + </when> </conditional> </xml> <token name="@DIAMOND_TAX_FILTER@"><![CDATA[ - #if $taxonlist + #if $filter_type.taxonlist --taxonlist '$taxonlist' #end if ]]></token> @@ -325,18 +325,18 @@ Indices and Metrics ___________________ -**AAIc - Average Amino Acid Identity coast** +**TAAI - Total Average Amino Acid Identity** -The AAIc is an attempt modify the AAI into a measure to compare proteomes for all annotated proteins. +The TAAI is an attempt modify the AAI into a measure to compare proteomes for all annotated proteins. Low identity hits will be considered, when they are usually removed by the traditional method. Proteins that have no match at all will be also considered, as having 0 identity match. It provides a way to compare the actual annotation and select organisms, even if more taxonomically distant, with proteins that could be relevant for the function determination in hypothetical proteins, as an example. For this the best hit is selected by the highest identity. -**AAIbd - Average Amino Acid Identity blast-diamond** +**AAI - Average Amino Acid Identity** -The AAIbd, is a implementation of a similar calculation to that of the original +The AAI, is a implementation of a similar calculation to that of the original AAI, but calculated only one way. It has by default a coverage and identity of 50 and 40 respectively. This values are also used by EzAAI, based in the recent study done by Nicholson et. all in 2020. The best hit is then selected by the the @@ -348,8 +348,8 @@ The following options might be used to calibrate this selection to the user's preference: -- Minimum Identity: Minimum Amino Acid Identity, for hit selection for the AAIbd calculation; -- Minimum Coverage: Minimum coverage, for hit selection for the AAIbd calculation. +- Minimum Identity: Minimum Amino Acid Identity, for hit selection for the AAI calculation; +- Minimum Coverage: Minimum coverage, for hit selection for the AAI calculation. **HITSPP - Hits Per Protein** @@ -371,10 +371,10 @@ **Batch alignment results** This is a non-optional output. It contains the all alignment search results for all proteins in the proteome. It can also be used to generated new outputs from the COAST Report tool, using different parameters. -**Summarized report** Is an HTML document that contains a list of filtered results ordered by AAIc. This report includes an heatmap visualization for protein identities. +**Summarized report** Is an HTML document that contains a list of filtered results ordered by TAAI. This report includes an heatmap visualization for protein identities. It also contains metadata for the COAST job. -**Best-hits table** Tabular file with all the individual selected best-hits for each protein in the proteome. These are the hits selected for the AAIc calculation. +**Best-hits table** Tabular file with all the individual selected best-hits for each protein in the proteome. These are the hits selected for the TAAI calculation. **Results table** Tabular file with aggregated metrics for each proteome match. Aggregated for taxid. |