Commit 62a6d5c9 authored by Jerome Mariette's avatar Jerome Mariette
Browse files

update blast_contamination_search documentation

parent 802ba9e3
......@@ -4,27 +4,31 @@ Search contamination using blast against databases. Calls blastall and a blast_f
<h3>inputs</h3>
<p>
<ul>
<li>input file: This program accepts fasta files as input.</li>
<li>databases: the list of path to the formated database separated by a coma (database shouldnt have a "." in there name).</li>
<li>ng6cfg file: The NG6 run config file the analyse belongs to.</li>
<li>project id: The NG6 project id the analyse belongs to.</li>
<li>input file list: the file list of files to clean.</li>
<li>input file: the single file to clean.</li>
<li>input directory: the directory within files to clean.</li>
<li>input extension: the following is only used when iterating over an input directory.</li>
<li>databases: the list of path to the formated database separated by a coma (database shouldnt have a "." in there name).</li>
<li>ng6cfg file: the NG6 run configuration file the analysis belongs to.</li>
<li>project id: the project id the analyse belongs to. </li>
</ul>
</p>
<h3>outputs</h3>
<p>
Outputs a name file with all sequences id detected as contaminant and the blast m8 file.
</p>
<ul>
<li>output m8 list: the list of blastn m8 files.</li>
<li>output names list: the list of contaminant names files.</li>
</ul>
<h3>parameters</h3>
<p>
<ul>
<li>expect: The blast e-value,</li>
<li>filter: Filter low complex region if set at T,</li>
<li>database matches: Blast number of databases matches,</li>
<li>descriptions: Blast number of descriptions,</li>
<li>other opts: Options to pass to blastall command,</li>
<li>pci: Min identity percent to consider the hit as contamination,</li>
<li>pcq: Min hit length percent to consider it as contamination,</li>
<li>analyse name: The analyse name to display in ng6,</li>
<li>analyse description: The analyse description to display in ng6,</li>
<li>results archive name: The results archive name to display in ng6.</li>
<li>expect: the blast e-value,</li>
<li>filter: filter low complex region if set at T,</li>
<li>database matches: blast number of databases matches,</li>
<li>descriptions: blast number of descriptions,</li>
<li>other opts: options to pass to blastall command,</li>
<li>pci: min identity percent to consider the hit as contamination,</li>
<li>pcq: min hit length percent to consider it as contamination,</li>
<li>analyse name: the analyse name to display in ng6,</li>
<li>analyse description: the analyse description to display in ng6,</li>
<li>results archive name: the results archive name to display in ng6.</li>
</ul>
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