Mercurial > repos > devteam > fastq_stats
diff fastq_stats.xml @ 2:e2cf940128d5 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
| author | devteam |
|---|---|
| date | Sat, 30 Sep 2017 13:55:30 -0400 |
| parents | daaf552153fe |
| children | b1cea1b2fcd0 |
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--- a/fastq_stats.xml Wed Nov 11 12:42:31 2015 -0500 +++ b/fastq_stats.xml Sat Sep 30 13:55:30 2017 -0400 @@ -1,25 +1,27 @@ -<tool id="fastq_stats" name="FASTQ Summary Statistics" version="1.0.0"> - <description>by column</description> - <requirements> - <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement> - </requirements> - <command interpreter="python">fastq_stats.py '$input_file' '$output_file' '${input_file.extension[len( 'fastq' ):]}'</command> - <inputs> - <param name="input_file" type="data" format="fastqsanger,fastqillumina,fastqsolexa,fastqcssanger" label="FASTQ File"/> - </inputs> - <outputs> - <data name="output_file" format="tabular" /> - </outputs> - <tests> - <test> - <param name="input_file" value="fastq_stats1.fastq" ftype="fastqsanger" /> - <output name="output_file" file="fastq_stats_1_out.tabular" /> - </test> - </tests> - <help> +<tool id="fastq_stats" name="FASTQ Summary Statistics" version="1.1.1"> + <description>by column</description> + <requirements> + <requirement type="package" version="1.1.1">galaxy_sequence_utils</requirement> + </requirements> + <command><![CDATA[ +gx-fastq-stats '$input_file' '$output_file' '${input_file.extension[len('fastq'):]}' + ]]></command> + <inputs> + <param name="input_file" type="data" format="fastqsanger,fastqillumina,fastqsolexa,fastqcssanger,fastqsanger.gz,fastqillumina.gz,fastqsolexa.gz,fastqcssanger.gz,fastqsanger.bz2,fastqillumina.bz2,fastqsolexa.bz2,fastqcssanger.bz2" label="FASTQ File"/> + </inputs> + <outputs> + <data name="output_file" format="tabular" /> + </outputs> + <tests> + <test> + <param name="input_file" value="fastq_stats1.fastq" ftype="fastqsanger" /> + <output name="output_file" file="fastq_stats_1_out.tabular" /> + </test> + </tests> + <help><![CDATA[ **What is does** -This tool creates summary statistics on a FASTQ file. +This tool creates summary statistics on a FASTQ file. .. class:: infomark @@ -53,24 +55,19 @@ For example:: #column count min max sum mean Q1 med Q3 IQR lW rW outliers A_Count C_Count G_Count T_Count N_Count other_bases other_base_count - 1 14336356 2 33 450600675 31.4306281875 32.0 33.0 33.0 1.0 31 33 2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30 4482314 2199633 4425957 3208745 19707 - 2 14336356 2 34 441135033 30.7703737965 30.0 33.0 33.0 3.0 26 34 2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25 4419184 2170537 4627987 3118567 81 - 3 14336356 2 34 433659182 30.2489127642 29.0 32.0 33.0 4.0 23 34 2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 4310988 2941988 3437467 3645784 129 - 4 14336356 2 34 433635331 30.2472490917 29.0 32.0 33.0 4.0 23 34 2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 4110637 3007028 3671749 3546839 103 - 5 14336356 2 34 432498583 30.167957813 29.0 32.0 33.0 4.0 23 34 2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 4348275 2935903 3293025 3759029 124 + 1 14336356 2 33 450600675 31.4306281875 32.0 33.0 33.0 1.0 31 33 2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30 4482314 2199633 4425957 3208745 19707 + 2 14336356 2 34 441135033 30.7703737965 30.0 33.0 33.0 3.0 26 34 2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25 4419184 2170537 4627987 3118567 81 + 3 14336356 2 34 433659182 30.2489127642 29.0 32.0 33.0 4.0 23 34 2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 4310988 2941988 3437467 3645784 129 + 4 14336356 2 34 433635331 30.2472490917 29.0 32.0 33.0 4.0 23 34 2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 4110637 3007028 3671749 3546839 103 + 5 14336356 2 34 432498583 30.167957813 29.0 32.0 33.0 4.0 23 34 2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 4348275 2935903 3293025 3759029 124 ----- .. class:: warningmark Adapter bases in color space reads are excluded from statistics. - ------- - - </help> - - <citations> - <citation type="doi">10.1093/bioinformatics/btq281</citation> - </citations> - + ]]></help> + <citations> + <citation type="doi">10.1093/bioinformatics/btq281</citation> + </citations> </tool>