| Previous changeset 51:3202911efdae (2014-12-05) Next changeset 53:f5a2e8308836 (2014-12-08) |
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Commit message:
Uploaded |
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modified:
miRPlant.xml microRNA.xml preProcess.xml |
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| diff -r 3202911efdae -r 8b8c356e6db5 miRPlant.xml --- a/miRPlant.xml Fri Dec 05 01:14:28 2014 -0500 +++ b/miRPlant.xml Fri Dec 05 01:28:46 2014 -0500 |
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| @@ -91,7 +91,7 @@ <param name="annotate_rfam" type="select" label="annotate rfam nocoding RNAs(excluding miRNA)"> <option value="yes" selected="true">yes</option> <option value="no">no</option> - </param> + </param> <when value="yes"> <!--param name="rfam" type="data" label="rfam sequence file" /--> <conditional name="reference_rfam"> @@ -114,19 +114,14 @@ <param name="v" type="integer" value="0" label="report end-to-end hits less than v mismatches for rfam mapping"/> - <conditional name="rfamresult"> - <param name="delet_rfam" type="select" label="delet rfam mapped reads"> - <option value="yes" selected="true">yes</option> - <option value="no">no</option> - </param> - </conditional> <!-- params --> - - + <param name="delet_rfam" type="select" label="delet rfam mapped reads"> + <option value="yes" selected="true">yes</option> + <option value="no">no</option> + </param> </when> - </conditional> <!-- params --> + </conditional> - <!--param name="input" format="tabular" type="data" label="input config file" /--> <param name="format" type="select" lable="raw data format" multiple="false"> <option value="fastq">Raw data is fastq. format</option> @@ -138,68 +133,6 @@ <option value="33" selected="true">Phred+33</option> </param> - <conditional name="reference_genome"> - <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> - <option value="indexed">Use a built-in index</option> - <option value="history">Use one from the history</option> - </param> - <when value="indexed"> - <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> - <options from_data_table="bowtie_indexes"> - <filter type="sort_by" column="2"/> - <validator type="no_options" message="No indexes are available for the selected input dataset"/> - </options> - </param> - </when> - <when value="history"> - <param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" /> - </when> - </conditional> - - <!--param type="data" name="index" label="genome sequence bowtie index"/--> - <conditional name="params"> - <param name="known_microRNA" type="select" label="Analysis known microRNAs(eg. from mirbase)"> - <option value="yes" selected="true">yes</option> - <option value="no">no</option> - </param> - <when value="yes"> - <param name="mat" type="data" label="mature microRNA sequence file" /> - <param name="pre" type="data" label="precursor microRNA sequence fie" /> - </when> - </conditional> <!-- params --> - - <conditional name="params"> - <param name="annotate_rfam" type="select" label="annotate rfam nocoding RNAs(excluding miRNA)"> - <option value="yes" selected="true">yes</option> - <option value="no">no</option> - </param> - <when value="yes"> - <!--param name="rfam" type="data" label="rfam sequence file" /--> - <when value="yes"> - <!--param name="rfam" type="data" label="rfam sequence file" /--> - <conditional name="reference_rfam"> - <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> - <option value="indexed">Use a built-in index</option> - <option value="history">Use one from the history</option> - </param> - <when value="indexed"> - <param name="index" type="select" label="Select a reference" help="If your reference of interest is not listed, contact the Galaxy team"> - <options from_data_table="rfam_bowtie_indexes"> - <filter type="sort_by" column="2"/> - <validator type="no_options" message="No indexes are available for the selected input dataset"/> - </options> - </param> - </when> - <when value="history"> - <param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select the reference" /> - </when> - </conditional> - - <param name="v" type="integer" value="0" label="report end-to-end hits less than v mismatches for rfam mapping"/> - </when> - </conditional> <!-- params --> - - <!--param type="data" name="idx2" label="rfam sequence bowtie index " --> <param name="a" type="text" value="ATCTCGTATG" label="3' adapter sequence" /> <param name="mapnt" type="integer" value="8" label="minimum adapter map nts" /> <param name="min" type="integer" value="19" label="minimum microRNA length" /> |
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| diff -r 3202911efdae -r 8b8c356e6db5 microRNA.xml --- a/microRNA.xml Fri Dec 05 01:14:28 2014 -0500 +++ b/microRNA.xml Fri Dec 05 01:28:46 2014 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="micrornas" name="microRNA" veision="1.0.0"> +<tool id="micrornas_v1" name="microRNA" veision="1.0.0"> <description>Plant microRNA analysis </description> <requirements> |
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| diff -r 3202911efdae -r 8b8c356e6db5 preProcess.xml --- a/preProcess.xml Fri Dec 05 01:14:28 2014 -0500 +++ b/preProcess.xml Fri Dec 05 01:28:46 2014 -0500 |
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| @@ -101,8 +101,6 @@ </param> <when value="yes"> <!--param name="rfam" type="data" label="rfam sequence file" /--> - <when value="yes"> - <!--param name="rfam" type="data" label="rfam sequence file" /--> <conditional name="reference_rfam"> <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> <option value="indexed">Use a built-in index</option> @@ -123,7 +121,9 @@ <param name="v" type="integer" value="0" label="report end-to-end hits less than v mismatches for rfam mapping"/> </when> - </conditional> <!-- params --> + </conditional> + + </inputs> |