Mercurial > repos > vimalkumarvelayudhan > riboplot
changeset 4:1901dcdc12ff
Move galaxy xml wrappers to top level
| author | Vimalkumar Velayudhan <vimal@biotechcoder.com> |
|---|---|
| date | Wed, 12 Aug 2015 09:44:36 +0100 |
| parents | 8e1efafa6277 |
| children | cef780bcce01 |
| files | galaxy/ribocount.xml galaxy/riboplot.xml ribocount.xml riboplot.xml |
| diffstat | 4 files changed, 84 insertions(+), 84 deletions(-) [+] |
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--- a/galaxy/ribocount.xml Wed Aug 12 09:27:45 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,30 +0,0 @@ -<tool id="ribocount" name="ribocount" version="0.1.0"> - <description>Get read counts for all transcripts in an alignment (BAM) - </description> - <requirements> - <requirement type="package" version="0.8.3">pysam</requirement> - </requirements> - <stdio> - <exit_code range="1:" level="fatal" description="Error" /> - </stdio> - <command interpreter="python">../riboplot/ribocount.py - --ribo_file "${ribo_file}" - --transcriptome_fasta "${transcriptome_fasta}" - --read_length "${read_length}" - --read_offset "${read_offset}" - --html_file "${html_file}" - --output_path "${html_file.files_path}" - ## --debug - </command> - <inputs> - <param name="ribo_file" type="data" format="bam" label="Ribo-Seq alignment file in BAM format"/> - <param name="transcriptome_fasta" type="data" format="fasta" label="FASTA format file of the transcriptome"/> - <param name="read_length" type="integer" label="Read length to consider" value="28"/> - <param name="read_offset" type="integer" label="Offset" value="0"/> - </inputs> - <outputs> - <data format="html" name="html_file" label="ribocount (HTML report)"/> - </outputs> - <help> - </help> -</tool>
--- a/galaxy/riboplot.xml Wed Aug 12 09:27:45 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,54 +0,0 @@ -<tool id="riboplot" name="riboplot" version="0.1.0"> - <description>Plot and output read counts for a single transcript in an alignment (BAM) - </description> - <requirements> - <requirement type="package" version="1.2.1">matplotlib</requirement> - <requirement type="package" version="0.8.3">pysam</requirement> - </requirements> - <stdio> - <exit_code range="1:" level="fatal" description="Error" /> - </stdio> - <command interpreter="python">../riboplot/riboplot.py - --ribo_file "${ribo_file}" - --transcriptome_fasta "${transcriptome_fasta}" - --transcript_name "${transcript_name}" - #if $rnacov.rnacov_select=="yes" - --rna_file "${rna_file}" - #end if - --read_length "${read_length}" - --read_offset "${read_offset}" - --html_file "${html_file}" - --output_path "${html_file.files_path}" - ## --debug - </command> - <inputs> - <param name="ribo_file" type="data" format="bam" label="Ribo-Seq alignment file in BAM format"/> - <param name="transcriptome_fasta" type="data" format="fasta" label="FASTA format file of the transcriptome"/> - <param name="transcript_name" type="text" label="Name of the transcript to plot (as in FASTA)" size="40"> - <validator type="expression" message="Please input a single transcript name">len(value.split(',')) == 1</validator> - <validator type="empty_field" message="Field requires a value"/> - <sanitizer> - <valid> - <add value="|"/> - </valid> - </sanitizer> - </param> - <conditional name="rnacov"> - <param name="rnacov_select" type="select" label="Include RNA Coverage"> - <option value="no">No</option> - <option value="yes">Yes</option> - </param> - <when value="yes"> - <param name="rna_file" type="data" format="bam" label="RNA-Seq alignment file in BAM format"/> - </when> - <when value="no" /> - </conditional> - <param name="read_length" type="integer" label="Read length to consider" value="28"/> - <param name="read_offset" type="integer" label="Offset" value="0"/> - </inputs> - <outputs> - <data format="html" name="html_file" label="riboplot (HTML report)"/> - </outputs> - <help> - </help> -</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ribocount.xml Wed Aug 12 09:44:36 2015 +0100 @@ -0,0 +1,30 @@ +<tool id="ribocount" name="ribocount" version="0.1.0"> + <description>Get read counts for all transcripts in an alignment (BAM) + </description> + <requirements> + <requirement type="package" version="0.8.3">pysam</requirement> + </requirements> + <stdio> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + <command interpreter="python">riboplot/ribocount.py + --ribo_file "${ribo_file}" + --transcriptome_fasta "${transcriptome_fasta}" + --read_length "${read_length}" + --read_offset "${read_offset}" + --html_file "${html_file}" + --output_path "${html_file.files_path}" + ## --debug + </command> + <inputs> + <param name="ribo_file" type="data" format="bam" label="Ribo-Seq alignment file in BAM format"/> + <param name="transcriptome_fasta" type="data" format="fasta" label="FASTA format file of the transcriptome"/> + <param name="read_length" type="integer" label="Read length to consider" value="28"/> + <param name="read_offset" type="integer" label="Offset" value="0"/> + </inputs> + <outputs> + <data format="html" name="html_file" label="ribocount (HTML report)"/> + </outputs> + <help> + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/riboplot.xml Wed Aug 12 09:44:36 2015 +0100 @@ -0,0 +1,54 @@ +<tool id="riboplot" name="riboplot" version="0.1.0"> + <description>Plot and output read counts for a single transcript in an alignment (BAM) + </description> + <requirements> + <requirement type="package" version="1.2.1">matplotlib</requirement> + <requirement type="package" version="0.8.3">pysam</requirement> + </requirements> + <stdio> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + <command interpreter="python">riboplot/riboplot.py + --ribo_file "${ribo_file}" + --transcriptome_fasta "${transcriptome_fasta}" + --transcript_name "${transcript_name}" + #if $rnacov.rnacov_select=="yes" + --rna_file "${rna_file}" + #end if + --read_length "${read_length}" + --read_offset "${read_offset}" + --html_file "${html_file}" + --output_path "${html_file.files_path}" + ## --debug + </command> + <inputs> + <param name="ribo_file" type="data" format="bam" label="Ribo-Seq alignment file in BAM format"/> + <param name="transcriptome_fasta" type="data" format="fasta" label="FASTA format file of the transcriptome"/> + <param name="transcript_name" type="text" label="Name of the transcript to plot (as in FASTA)" size="40"> + <validator type="expression" message="Please input a single transcript name">len(value.split(',')) == 1</validator> + <validator type="empty_field" message="Field requires a value"/> + <sanitizer> + <valid> + <add value="|"/> + </valid> + </sanitizer> + </param> + <conditional name="rnacov"> + <param name="rnacov_select" type="select" label="Include RNA Coverage"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="yes"> + <param name="rna_file" type="data" format="bam" label="RNA-Seq alignment file in BAM format"/> + </when> + <when value="no" /> + </conditional> + <param name="read_length" type="integer" label="Read length to consider" value="28"/> + <param name="read_offset" type="integer" label="Offset" value="0"/> + </inputs> + <outputs> + <data format="html" name="html_file" label="riboplot (HTML report)"/> + </outputs> + <help> + </help> +</tool>