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comparison stringtie.xml @ 4:df42808cc33a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit ba7b53894c61fea9a93550f865e9ed2753a904cf
author iuc
date Wed, 12 Aug 2015 07:07:40 -0400
parents 520e0988ec1c
children f504b3b7e49d
comparison
equal deleted inserted replaced
3:48b891c1c2aa 4:df42808cc33a
1 <tool id="stringtie" name="StringTie" version="1.0.3"> 1 <tool id="stringtie" name="StringTie" version="1.0.4">
2 <description>transcript assembly and quantification</description> 2 <description>transcript assembly and quantification</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.0.3">stringtie</requirement> 4 <requirement type="package" version="1.0.4">stringtie</requirement>
5 </requirements> 5 </requirements>
6 <command><![CDATA[ 6 <command><![CDATA[
7 stringtie "$input_bam" 7 stringtie "$input_bam"
8 -o "$output_gtf" 8 -o "$output_gtf"
9 -p "\${GALAXY_SLOTS:-1}" 9 -p "\${GALAXY_SLOTS:-1}"
19 -m "$option_set.min_tlen" 19 -m "$option_set.min_tlen"
20 -a "$option_set.min_anchor_len" 20 -a "$option_set.min_anchor_len"
21 -j "$option_set.min_anchor_cov" 21 -j "$option_set.min_anchor_cov"
22 -c "$option_set.min_bundle_cov" 22 -c "$option_set.min_bundle_cov"
23 -s "$option_set.maxcov" 23 -s "$option_set.maxcov"
24 -g "$option_set.bdist" 24 -g "$option_set.bdist"
25 -M "$option_set.bundle_fraction" $option_set.sensitive $option_set.disable_trimming 25 -M "$option_set.bundle_fraction" $option_set.sensitive $option_set.disable_trimming
26 #end if 26 #end if
27 ]]> 27 ]]>
28 </command> 28 </command>
29 <inputs> 29 <inputs>
85 <tests> 85 <tests>
86 <test> 86 <test>
87 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> 87 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
88 <param name="use_guide" value="no" /> 88 <param name="use_guide" value="no" />
89 <param name="options" value="default" /> 89 <param name="options" value="default" />
90 <output file="stringtie_out1.gtf" ftype="gtf" name="output_gtf" /> 90 <output file="stringtie_out1.gtf" ftype="gtf" name="output_gtf" lines_diff="2" />
91 </test> 91 </test>
92 <test> 92 <test>
93 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> 93 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
94 <param name="use_guide" value="no" /> 94 <param name="use_guide" value="no" />
95 <param name="options" value="advanced" /> 95 <param name="options" value="advanced" />
96 <param name="fraction" value="0.17" /> 96 <param name="fraction" value="0.17" />
97 <output file="stringtie_out2.gtf" ftype="gtf" name="output_gtf" /> 97 <output file="stringtie_out2.gtf" ftype="gtf" name="output_gtf" lines_diff="2" />
98 </test> 98 </test>
99 <test> 99 <test>
100 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> 100 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
101 <param name="use_guide" value="yes" /> 101 <param name="use_guide" value="yes" />
102 <param name="guide_gff" value="stringtie_in.gtf" /> 102 <param name="guide_gff" value="stringtie_in.gtf" />
103 <param name="options" value="default" /> 103 <param name="options" value="default" />
104 <output file="stringtie_out3.gtf" ftype="gtf" name="output_gtf" /> 104 <output file="stringtie_out3.gtf" ftype="gtf" name="output_gtf" lines_diff="2" />
105 </test> 105 </test>
106 <test> 106 <test>
107 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> 107 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
108 <param name="use_guide" value="yes" /> 108 <param name="use_guide" value="yes" />
109 <param name="guide_gff" value="stringtie_in.gtf" /> 109 <param name="guide_gff" value="stringtie_in.gtf" />
110 <param name="options" value="advanced" /> 110 <param name="options" value="advanced" />
111 <param name="fraction" value="0.17" /> 111 <param name="fraction" value="0.17" />
112 <output file="stringtie_out4.gtf" ftype="gtf" name="output_gtf" /> 112 <output file="stringtie_out4.gtf" ftype="gtf" name="output_gtf" lines_diff="2" />
113 </test> 113 </test>
114 <test> 114 <test>
115 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> 115 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
116 <param name="use_guide" value="yes" /> 116 <param name="use_guide" value="yes" />
117 <param name="output_ballgown" value="yes" /> 117 <param name="output_ballgown" value="yes" />
120 <output file="ballgown/e_data.ctab" ftype="tabular" name="exon_expression" /> 120 <output file="ballgown/e_data.ctab" ftype="tabular" name="exon_expression" />
121 <output file="ballgown/i_data.ctab" ftype="tabular" name="intron_expression" /> 121 <output file="ballgown/i_data.ctab" ftype="tabular" name="intron_expression" />
122 <output file="ballgown/t_data.ctab" ftype="tabular" name="transcript_expression" /> 122 <output file="ballgown/t_data.ctab" ftype="tabular" name="transcript_expression" />
123 <output file="ballgown/e2t.ctab" ftype="tabular" name="exon_transcript_mapping" /> 123 <output file="ballgown/e2t.ctab" ftype="tabular" name="exon_transcript_mapping" />
124 <output file="ballgown/i2t.ctab" ftype="tabular" name="intron_transcript_mapping" /> 124 <output file="ballgown/i2t.ctab" ftype="tabular" name="intron_transcript_mapping" />
125 <output file="stringtie_out5.gtf" ftype="gtf" name="output_gtf" /> 125 <output file="stringtie_out5.gtf" ftype="gtf" name="output_gtf" lines_diff="2" />
126 <output file="stringtie_out_coverage.gtf" ftype="gff3" name="coverage" /> 126 <output file="stringtie_out_coverage.gtf" ftype="gff3" name="coverage" />
127 </test> 127 </test>
128 </tests> 128 </tests>
129 <help> 129 <help>
130 <![CDATA[ 130 <![CDATA[