Mercurial > repos > iuc > meme_dreme
diff dreme.xml @ 6:fd05b142b3a3 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
| author | iuc |
|---|---|
| date | Thu, 29 Aug 2024 10:19:55 +0000 |
| parents | f33d77dcacce |
| children |
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--- a/dreme.xml Sat Apr 09 08:32:58 2022 +0000 +++ b/dreme.xml Thu Aug 29 10:19:55 2024 +0000 @@ -1,11 +1,9 @@ -<tool id="meme_dreme" name="DREME" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> +<tool id="meme_dreme" name="DREME" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>- Discriminative Regular Expression Motif Elicitation</description> <macros> <import>macros.xml</import> </macros> - <expand macro="requirements"> - <requirement type="package" version="2.7">python</requirement> - </expand> + <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ @CHECK_NON_COMMERCIAL_USE@ dreme @@ -32,30 +30,23 @@ #end if ]]></command> <inputs> - <param name="pos_fasta_file" type="data" format="fasta" label="Positive FASTA sequence file" argument="-p" - help="positive (primary) sequence file"/> + <param name="pos_fasta_file" argument="-p" type="data" format="fasta" label="Positive FASTA sequence file" help="positive (primary) sequence file"/> <param name="alphabet_type" type="select" label="Type of sequence alphabet"> <option value="-dna" selected="true">DNA (default)</option> <option value="-rna">RNA</option> <option value="-protein">Protein</option> </param> - <param argument="-norc" label="Check reverse complement" type="boolean" - truevalue="" falsevalue="-norc" checked="False" - help="Search for motifs also on reverse complement strand"/> + <param argument="-norc" type="boolean" truevalue="" falsevalue="-norc" checked="False" label="Check reverse complement" help="Search for motifs also on reverse complement strand"/> <conditional name="neg_set_type"> <param name="neg_set_type_selector" type="select" label="Negative set definition"> <option value="shuffle_negs" selected="true">Shuffle positive sequences</option> <option value="supply_negs">Supply negative sequences</option> </param> <when value="shuffle_negs"> - <param name="pos_shuffle_seed" type="integer" value="1" - label="Seed for shuffling positive sequences" argument="-s" - help="(default: 1)"/> + <param name="pos_shuffle_seed" argument="-s" type="integer" value="1" label="Seed for shuffling positive sequences" help="(default: 1)"/> </when> <when value="supply_negs"> - <param name="neg_fasta_file" type="data" format="fasta" - label="Negative FASTA sequence file" argument="-n" - help="negative (control) sequence file (default: positive sequences are shuffled to create the negative set)"/> + <param name="neg_fasta_file" argument="-n" type="data" format="fasta" label="Negative FASTA sequence file" help="negative (control) sequence file (default: positive sequences are shuffled to create the negative set)"/> </when> </conditional> <conditional name="options_type"> @@ -63,31 +54,19 @@ <option value="basic" selected="true">Basic</option> <option value="advanced">Advanced</option> </param> - <when value="basic" /> + <when value="basic"/> <when value="advanced"> - <param name="e_value_thr" type="float" value="0.05" - label="stop if motif E-value > e" argument="-e" - help="stop if motif E-value > given threshold (default: 0.05)"> - <validator type="expression" message="Set e-value must be > 0.">value is not None and value > 0</validator> + <param name="e_value_thr" argument="-e" type="float" value="0.05" label="stop if motif E-value > e" help="stop if motif E-value > given threshold (default: 0.05)"> + <validator type="expression" message="Set e-value must be > 0.">value is not None and value > 0</validator> </param> - <param name="motif_min_k" type="integer" value="3" min="1" - label="Minimum width of core motif" argument="-mink" - help="minimum width of core motif (default: 3)"/> - <param name="motif_max_k" type="integer" value="8" min="1" - label="Maximum width of core motif" argument="-maxk" - help="maximum width of core motif (default: 8)"/> - <param name="stop_m_motifs" type="integer" optional="True" min="1" - label="Stop if m motifs have been output" argument="-m" - help="stop if m motifs have been output (default: only stop at E-value threshold)"/> - <param name="stop_t_seconds" type="integer" optional="True" min="1" - label="Stop if the specified time has elapsed" argument="-t" - help="stop if the specified time has elapsed (default: only stop at E-value threshold)"/> - <param name="nr_res_generalize" type="integer" value="100" min="1" - label="Number of REs to generalize" argument="-g" - help="number of REs to generalize (default: 100) (Hint: Increasing n will make the motif search more thoroughly at some cost in speed)"/> + <param name="motif_min_k" argument="-mink" type="integer" min="1" value="3" label="Minimum width of core motif" help="minimum width of core motif (default: 3)"/> + <param name="motif_max_k" argument="-maxk" type="integer" min="1" value="8" label="Maximum width of core motif" help="maximum width of core motif (default: 8)"/> + <param name="stop_m_motifs" argument="-m" type="integer" min="1" optional="True" label="Stop if m motifs have been output" help="stop if m motifs have been output (default: only stop at E-value threshold)"/> + <param name="stop_t_seconds" argument="-t" type="integer" min="1" optional="True" label="Stop if the specified time has elapsed" help="stop if the specified time has elapsed (default: only stop at E-value threshold)"/> + <param name="nr_res_generalize" argument="-g" type="integer" min="1" value="100" label="Number of REs to generalize" help="number of REs to generalize (default: 100) (Hint: Increasing n will make the motif search more thoroughly at some cost in speed)"/> </when> </conditional> - <param name="non_commercial_use" label="I certify that I am not using this tool for commercial purposes." type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="False"> + <param name="non_commercial_use" type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="False" label="I certify that I am not using this tool for commercial purposes."> <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator> </param> </inputs> @@ -102,9 +81,34 @@ <param name="alphabet_type" value="-rna"/> <param name="norc" value="false"/> <param name="non_commercial_use" value="True"/> - <output name="html_outfile" file="dreme_output_test1.html" compare="contains"/> - <output name="txt_outfile" file="dreme_output_test1.txt" compare="contains"/> - <output name="xml_outfile" file="dreme_output_test1.xml" compare="contains"/> + <output name="html_outfile"> + <assert_contents> + <has_text text="pvalue"/> + <has_text text="UUUUCC"/> + <has_text text="evalue"/> + <has_text text="matches"/> + <has_text text="DREME"/> + </assert_contents> + </output> + <output name="txt_outfile"> + <assert_contents> + <has_text text="RNA-LIKE"/> + <has_text text="shuffled"/> + <has_text text="0.221"/> + <has_text text="DREME"/> + <has_text text="letter-probability matrix"/> + <has_n_lines n="84"/> + </assert_contents> + </output> + <output name="xml_outfile"> + <assert_contents> + <has_text text="Adenine"/> + <has_text text="command_line"/> + <has_text text="Uracil"/> + <has_text text="DREME"/> + <has_text text="evalue"/> + </assert_contents> + </output> </test> <test> <param name="pos_fasta_file" value="dreme_test_sites.fa" ftype="fasta"/> @@ -115,9 +119,35 @@ <param name="motif_min_k" value="4"/> <param name="motif_max_k" value="10"/> <param name="non_commercial_use" value="True"/> - <output name="html_outfile" file="dreme_output_test2.html" compare="contains"/> - <output name="txt_outfile" file="dreme_output_test2.txt" compare="contains"/> - <output name="xml_outfile" file="dreme_output_test2.xml" compare="contains"/> + <output name="html_outfile"> + <assert_contents> + <has_text text="shuffled positive sequences"/> + <has_text text="UUCUCU"/> + <has_text text="YAGG"/> + <has_text text="runtime"/> + <has_text text="DREME"/> + <has_text text="ACGU"/> + </assert_contents> + </output> + <output name="txt_outfile"> + <assert_contents> + <has_text text="RNA-LIKE"/> + <has_text text="from shuffled positives"/> + <has_text text="MOTIF UUYUCY DREME"/> + <has_text text="probability"/> + <has_text text="YAGG"/> + <has_n_lines n="68"/> + </assert_contents> + </output> + <output name="xml_outfile"> + <assert_contents> + <has_text text="Purine"/> + <has_text text="1000"/> + <has_text text="shuffled"/> + <has_text text="rna"/> + <has_text text="evalue"/> + </assert_contents> + </output> </test> </tests> <help><![CDATA[