Mercurial > repos > bgruening > sailfish
changeset 0:2306a9c40c37 draft
Uploaded
| author | bgruening |
|---|---|
| date | Sat, 12 Jul 2014 03:28:47 -0400 |
| parents | |
| children | 8792dd3c72b6 |
| files | README.rst sailfish.xml tool_dependencies.xml |
| diffstat | 3 files changed, 140 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Sat Jul 12 03:28:47 2014 -0400 @@ -0,0 +1,53 @@ +Galaxy wrappers for sailfish +===================================== + +These wrappers are copyright 2014 by Björn Grüning and additional contributors. +All rights reserved. See the licence text below. + +Currently tested with sailfish 0.6.3. + + +Automated Installation +====================== + +Galaxy should be able to automatically install the sailfish for you. + + +History +======= + +======== ====================================================================== +Version Changes +-------- ---------------------------------------------------------------------- +v0.6.3.0 - First release + +======== ====================================================================== + + +Bug Reports +=========== + +You can file an issue here https://github.com/bgruening/galaxytools/issues or ask +us on the Galaxy development list http://lists.bx.psu.edu/listinfo/galaxy-dev + + +Licence (MIT) +============= + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sailfish.xml Sat Jul 12 03:28:47 2014 -0400 @@ -0,0 +1,81 @@ +<tool id="sailfish" name="Sailfish" version="0.6.3.0"> + <description>transcript quantification from RNA-seq data</description> + <version_command>sailfish -version</version_command> + <expand macro="requirements" /> + <command> +<![CDATA[ + sailfish quant -i $index_dir + #if $single_or_paired-single_or_paired_opts == 'single': + -l "TYPE=SE" + -r $single_or_paired_opts.input_singles + #else: + -1 $single_or_paired_opts.input_mate1 + -2 $single_or_paired_opts.input_mate2 + #if $single_or_paired_opts.orientation == "same": + -l "TYPE=PE:O=>>" + #elif $single_or_paired_opts.orientation == "away": + -l "TYPE=PE:O=<>" + #else: + -l "TYPE=PE:O=><" + #end if + #end if +-o <quant_dir> + +]]> + </command> + <expand macro="stdio" /> + <inputs> + <conditional name="single_or_paired"> + <param name="single_or_paired_opts" type="select" label="Is this library mate-paired?"> + <option value="single">Single-end</option> + <option value="paired">Paired-end</option> + </param> + <when value="single"> + <param name="input_singles" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ file." /> + </when> + <when value="paired"> + <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 1" help="FASTQ file." /> + <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 2" help="FASTQ file." /> + <param name="orientation" type="select" label="Relative orientation of reads within a pair"> + <option value="same">Mates are oriented in the same direction</option> + <option value="away">Mates are oriented away from each other</option> + <option value="toward" selected="True">Mates are oriented toward each other</option> + </param> + </when> + </conditional> + + <expand macro="input_conditional_index" /> + + </inputs> + <outputs> + <data name="output1" format="tabular" label="${blast_type.value} $query.name vs @ON_DB_SUBJECT@"> + <expand macro="output_change_format" /> + </data> + </outputs> + <tests> + </tests> + <help> +<![CDATA[ +**What it does** + + +The first option >> denotes that the mates are oriented in the same direction --- e.g. if the 5' end of mate 1 is +upstream from the 3' end, then the 5' end of mate 2 is upstream from its 3' end and vice-versa. + +The second option <> denotes that the mates are oriented away from each other. This implies that start +of mate1 is closer to start of mate 2 than the end of mate 2, etc. + +The third option >< is, perhaps, the most common relative orientation. It denotes that the mates are +oriented toward each other, so that the start of mate 1 is farther from the start of mate 2 than it is from the end of mate 2 and vice-versa. + +------- + +**References** + +If you use this Galaxy tool in work leading to a scientific publication please +cite the following: + + +]]> + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Sat Jul 12 03:28:47 2014 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="sailfish" version="0.6.3"> + <repository changeset_revision="6453a4f36990" name="package_sailfish_0_6" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>