Mercurial > repos > pitagora > sailfish_linux
changeset 1:0283d2d3f8d6
commit
| author | pitagora <ryota.yamanaka@riken.jp> |
|---|---|
| date | Thu, 26 Mar 2015 13:18:34 +0900 |
| parents | 05154d5ffbdb |
| children | d474f67ae32f |
| files | README.rst sailfish.xml sailfish_linux.xml tool_dependencies.xml tool_dependency.xml |
| diffstat | 5 files changed, 129 insertions(+), 136 deletions(-) [+] |
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--- a/README.rst Thu Mar 26 13:15:17 2015 +0900 +++ b/README.rst Thu Mar 26 13:18:34 2015 +0900 @@ -1,53 +1,9 @@ -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 -====================== +This code is originated from the followings. Prease refer them for the licence information: -Galaxy should be able to automatically install the sailfish for you. - - -History -======= - -======== ====================================================================== -Version Changes --------- ---------------------------------------------------------------------- -v0.6.3.0 - First release - -======== ====================================================================== - +Mika Yoshimura's code: https://github.com/myoshimura080822/galaxy-mytools_sailfish -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) -============= +Björn Grüning's code: https://github.com/bgruening/galaxytools/tree/master/tools/sailfish -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: +If you use this Galaxy tool in work leading to a scientific publication please cite the following: -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. +Sailfish: http://www.cs.cmu.edu/~ckingsf/software/sailfish/
--- a/sailfish.xml Thu Mar 26 13:15:17 2015 +0900 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,81 +0,0 @@ -<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/sailfish_linux.xml Thu Mar 26 13:18:34 2015 +0900 @@ -0,0 +1,117 @@ + +<tool id="sailfish_linux" name="Sailfish" version="0.6.3"> + <description>transcript quantification from RNA-seq data</description> + <version_command>sailfish -version</version_command> + <!-- <expand macro="requirements" /> --> + <requirements> + <requirement type="package" version="0.6.3">sailfish_linux</requirement> + </requirements> + <command> +<![CDATA[ + sailfish quant -i ${filter(lambda x: str(x[0]) == str($index_path), $__app__.tool_data_tables['sailfish_custom_indexes'].get_fields())[0][-1]} + #if $single_or_paired.single_or_paired_opts == 'single': + -l "T=SE" + -r $single_or_paired.input_singles + #else: + #if $single_or_paired.orientation == "same": + #if $single_or_paired.strandedness == "sense": + -l "T=PE:O=>>:S=S" + #elif $single_or_paired.strandedness == "antisense": + -l "T=PE:O=>>:S=A" + #else: + -l "T=PE:O=>>:S=U" + #end if + #elif $single_or_paired.orientation == "away": + #if $single_or_paired.strandedness == "sense": + -l "T=PE:O=<>:S=S" + #elif $single_or_paired.strandedness == "antisense": + -l "T=PE:O=<>:S=A" + #else: + -l "T=PE:O=<>:S=U" + #end if + #else: + #if $single_or_paired.strandedness == "sense": + -l "T=PE:O=><:S=S" + #elif $single_or_paired.strandedness == "antisense": + -l "T=PE:O=><:S=A" + #else: + -l "T=PE:O=><:S=U" + #end if + #end if + -1 $single_or_paired.input_mate1 + -2 $single_or_paired.input_mate2 + #end if + -o ./ >> $log 2>&1 +]]> + </command> + <!-- <expand macro="stdio" /> --> + <inputs> + <param name="index_path" type="select" label="Select a sailfish index"> + <options from_data_table="sailfish_custom_indexes"> + <validator type="no_options" message="No index are available"/> + </options> + </param> + <conditional name="single_or_paired"> + <param name="single_or_paired_opts" type="select" label="Is this library mate-paired?"> + <option value="single">Single-end</option> + <option value="paired">Paired-end</option> + </param> + <when value="single"> + <param name="input_singles" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ file." /> + </when> + <when value="paired"> + <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 1" help="FASTQ file." /> + <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 2" help="FASTQ file." /> + <param name="orientation" type="select" label="Relative orientation of reads within a pair"> + <option value="same">Mates are oriented in the same direction</option> + <option value="away">Mates are oriented away from each other</option> + <option value="toward" selected="True">Mates are oriented toward each other</option> + </param> + <param name="strandedness" type="select" label="Specifies the strandedness of the reads"> + <option value="sense">sense strand</option> + <option value="antisense">antisense strand</option> + <option value="unknown" selected="True">unknown strandedness</option> + </param> + </when> + </conditional> + <!-- <expand macro="input_conditional_index" /> --> + </inputs> + <outputs> + <data name="log" format="txt" label="${tool.name} on ${on_string}: log"/> + <data name="quant" format="txt" from_work_dir="quant.sf" label="${tool.name} on ${on_string}: quant"/> + <data name="quant_bias_corrected" format="txt" from_work_dir="quant_bias_corrected.sf" label="${tool.name} on ${on_string}: quant_bias_corrected"/> + <data name="reads_count_info" format="txt" from_work_dir="reads.count_info" label="${tool.name} on ${on_string}: reads_count_info"/> + </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** + +This code is originated from the followings. Prease refer them for the licence information: + +Mika Yoshimura's code: https://github.com/myoshimura080822/galaxy-mytools_sailfish + +Björn Grüning's code: https://github.com/bgruening/galaxytools/tree/master/tools/sailfish + +If you use this Galaxy tool in work leading to a scientific publication please cite the following: + +Sailfish: http://www.cs.cmu.edu/~ckingsf/software/sailfish/ + +]]> + </help> +</tool> +
--- a/tool_dependencies.xml Thu Mar 26 13:15:17 2015 +0900 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -<?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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependency.xml Thu Mar 26 13:18:34 2015 +0900 @@ -0,0 +1,7 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="sailfish_linux" version="0.6.3"> + <repository changeset_revision="2c66da813a79" name="package_sailfish_linux_0_6_3" owner="pitagora" prior_installation_required="False" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </package> + </package> +</tool_dependency>