Mercurial > repos > mingchen0919 > aurora_dustmasker
comparison rmarkdown_report.xml @ 1:e0828838e0f3 draft default tip
update
author | mingchen0919 |
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date | Fri, 09 Nov 2018 15:25:01 -0500 |
parents | b8c76b06d724 |
children |
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0:b8c76b06d724 | 1:e0828838e0f3 |
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21 | 21 |
22 -o $report | 22 -o $report |
23 -d $report.files_path | 23 -d $report.files_path |
24 | 24 |
25 -A $input_fasta | 25 -A $input_fasta |
26 -B $level | 26 -B $window_length |
27 -C $linker | 27 -C $level |
28 -D $input_format | 28 -D $linker |
29 -E $output_format | 29 -E $input_format |
30 -F $parse_seqids | 30 -F $output_format |
31 -G $parse_seqids | |
31 | 32 |
32 -G $out | 33 -H $out |
33 | 34 |
34 | 35 |
35 ]]></command> | 36 ]]></command> |
36 <inputs> | 37 <inputs> |
37 <param type="data" name="input_fasta" argument="-in" label="Input file name" optional="False" format="fasta,fa"/><param type="integer" name="level" argument="-level" label="DUST level (score threshold for subwindows)" optional="False" value="20"/><param type="integer" name="linker" argument="-linker" label="DUST linker (how close masked intervals should be to get merged together)." optional="False" value="1"/><param type="integer" name="window_length" argument="window" label="DUST window length" optional="False" value="64"/><param type="select" name="input_format" label="Input format (possible values: fasta, blastdb)" optional="False" multiple="False"><option value="input_format_fasta" selected="true">fasta</option><option value="input_format_blastdb" selected="false">blastdb</option></param><param type="select" name="output_format" argument="-outfmt" label="Output format" optional="False" multiple="False"><option value="output_acclist" selected="false">acclist</option><option value="output_fasta" selected="false">fasta</option><option value="output_interval" selected="false">interval</option><option value="output_maskinfo_asn1_bin" selected="false">maskinfo_asn1_bin</option><option value="output_maskinfo_asn1_text" selected="false">maskinfo_asn1_text</option><option value="output_maskinfo_xml" selected="false">maskinfo_xml</option><option value="output_seqloc_asn1_bin" selected="false">output_seqloc_asn1_bin</option><option value="output_seqloc_asn1_text" selected="false">seqloc_asn1_text</option><option value="output_seqloc_xml" selected="false">seqloc_xml</option></param><param type="boolean" name="parse_seqids" argument="-parse_seqids" label="Parse Seq-ids in FASTA input" optional="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/></inputs> | 38 <param type="data" name="input_fasta" argument="-in" label="Input file name" optional="False" format="fasta,fa"/><param type="integer" name="level" argument="-level" label="DUST level (score threshold for subwindows)" optional="False" value="20"/><param type="integer" name="linker" argument="-linker" label="DUST linker (how close masked intervals should be to get merged together)." optional="False" value="1"/><param type="integer" name="window_length" argument="window" label="DUST window length" optional="False" value="64"/><param type="select" name="input_format" label="Input format (possible values: fasta, blastdb)" optional="False" multiple="False"><option value="fasta" selected="true">fasta</option><option value="blastdb" selected="false">blastdb</option></param><param type="select" name="output_format" argument="-outfmt" label="Output format" optional="False" multiple="False"><option value="acclist" selected="false">acclist</option><option value="fasta" selected="true">fasta</option><option value="interval" selected="false">interval</option><option value="maskinfo_asn1_bin" selected="false">maskinfo_asn1_bin</option><option value="maskinfo_asn1_text" selected="false">maskinfo_asn1_text</option><option value="maskinfo_xml" selected="false">maskinfo_xml</option><option value="seqloc_asn1_bin" selected="false">output_seqloc_asn1_bin</option><option value="seqloc_asn1_text" selected="false">seqloc_asn1_text</option><option value="seqloc_xml" selected="false">seqloc_xml</option></param><param type="boolean" name="parse_seqids" argument="-parse_seqids" label="Parse Seq-ids in FASTA input" optional="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/></inputs> |
38 <outputs> | 39 <outputs> |
39 <data format="html" name="report" label="${tool.name} report on ${on_string}"/><data name="out" label="${tool.name} on ${on_string}" hidden="false"/></outputs> | 40 <data format="html" name="report" label="${tool.name} report on ${on_string}"/><data name="out" format="fasta" label="${tool.name} on ${on_string}" hidden="false"/></outputs> |
40 <citations> | 41 <citations> |
41 <citation type="bibtex"><![CDATA[ | 42 <citation type="bibtex"><![CDATA[ |
42 @article{allaire2016rmarkdown, | 43 @article{allaire2016rmarkdown, |
43 title={rmarkdown: Dynamic Documents for R, 2016}, | 44 title={rmarkdown: Dynamic Documents for R, 2016}, |
44 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff | 45 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff |