| Previous changeset 13:a4a170bc040f (2017-12-20) Next changeset 15:6d9f127da28f (2018-01-26) |
|
Commit message:
Uploaded |
|
modified:
sRNAPipe.xml |
| b |
| diff -r a4a170bc040f -r cc66a625989f sRNAPipe.xml --- a/sRNAPipe.xml Wed Dec 20 10:15:21 2017 -0500 +++ b/sRNAPipe.xml Fri Jan 26 08:08:24 2018 -0500 |
| b |
| @@ -21,6 +21,8 @@ #if $tRNAs.refGenomeSource == "history": --tRNAs "${tRNAs.ownFile}" --build_tRNAs + #elif $tRNAs.refGenomeSource == "none": + --tRNAs "None" #else: --tRNAs "${tRNAs.indices.fields.path}" #end if @@ -28,10 +30,21 @@ #if $snRNAs.refGenomeSource == "history": --snRNAs "${snRNAs.ownFile}" --build_snRNAs + #elif $snRNAs.refGenomeSource == "none": + --snRNAs "None" #else: --snRNAs "${snRNAs.indices.fields.path}" #end if + #if $rRNAs.refGenomeSource == "history": + --rRNAs "${rRNAs.ownFile}" + --build_rRNAs + #elif $rRNAs.refGenomeSource == "none": + --rRNAs "None" + #else: + --rRNAs "${rRNAs.indices.fields.path}" + #end if + #if $miRNAs.refGenomeSource == "history": --miRNAs "${miRNAs.ownFile}" --build_miRNAs @@ -53,13 +66,6 @@ --TE "${TE.indices.fields.path}" #end if - #if $rRNAs.refGenomeSource == "history": - --rRNAs "${rRNAs.ownFile}" - --build_rRNAs - #else: - --rRNAs "${rRNAs.indices.fields.path}" - #end if - --si_min $si_min --si_max $si_max --pi_min $pi_min @@ -102,6 +108,23 @@ <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" /> </when> </conditional> + <conditional name="transcripts"> + <param name="refGenomeSource" type="select" label="Will you select transcripts database from your history or use a built-in index?"> + <option value="indexed">Use a built-in index</option> + <option value="history">Use one from the history</option> + </param> + <when value="indexed"> + <param name="indices" type="select" label="Select a transcripts reference"> + <options from_data_table="bwa_indexes"> + <filter type="sort_by" column="2" /> + <validator type="no_options" message="No indexes are available" /> + </options> + </param> + </when> + <when value="history"> + <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" /> + </when> + </conditional> <conditional name="TE"> <param name="refGenomeSource" type="select" label="Will you select TE database from your history or use a built-in index?"> <option value="indexed">Use a built-in index</option> @@ -140,6 +163,7 @@ <param name="refGenomeSource" type="select" label="Will you select snRNA database from your history or use a built-in index?"> <option value="indexed">Use a built-in index</option> <option value="history">Use one from the history</option> + <option value="none">None</option> </param> <when value="indexed"> <param name="indices" type="select" label="Select a snRNAs reference"> @@ -157,6 +181,7 @@ <param name="refGenomeSource" type="select" label="Will you select rRNAs database from your history or use a built-in index?"> <option value="indexed">Use a built-in index</option> <option value="history">Use one from the history</option> + <option value="none">None</option> </param> <when value="indexed"> <param name="indices" type="select" label="Select a rRNAs reference"> @@ -174,6 +199,7 @@ <param name="refGenomeSource" type="select" label="Will you select tRNA database from your history or use a built-in index?"> <option value="indexed">Use a built-in index</option> <option value="history">Use one from the history</option> + <option value="none">None</option> </param> <when value="indexed"> <param name="indices" type="select" label="Select a tRNA reference"> @@ -187,23 +213,7 @@ <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" /> </when> </conditional> - <conditional name="transcripts"> - <param name="refGenomeSource" type="select" label="Will you select transcripts database from your history or use a built-in index?"> - <option value="indexed">Use a built-in index</option> - <option value="history">Use one from the history</option> - </param> - <when value="indexed"> - <param name="indices" type="select" label="Select a transcripts reference"> - <options from_data_table="bwa_indexes"> - <filter type="sort_by" column="2" /> - <validator type="no_options" message="No indexes are available" /> - </options> - </param> - </when> - <when value="history"> - <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" /> - </when> - </conditional> + <param name="min" type="integer" value="18" label="minimum read size"/> <param name="max" type="integer" value="29" label="maximum read size"/> <param name="si_min" type="integer" value="21" label="lower bound of siRNA range"/> |