| Previous changeset 0:08256557922f (2015-10-13) Next changeset 2:8d09f8be269e (2020-06-16) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 8301d37348be25a038b3c63b049b1178d05f5003" |
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modified:
velvetg.xml velveth.xml |
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removed:
tool_dependencies.xml velvetg_wrapper.py velveth_wrapper.py |
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| diff -r 08256557922f -r 5da9a0e2fb2d tool_dependencies.xml --- a/tool_dependencies.xml Tue Oct 13 16:38:28 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="velvet" version="1.2.10"> - <repository changeset_revision="93d32326537b" name="package_velvet_1_2_10" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |
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| diff -r 08256557922f -r 5da9a0e2fb2d velvetg.xml --- a/velvetg.xml Tue Oct 13 16:38:28 2015 -0400 +++ b/velvetg.xml Wed Feb 12 11:16:32 2020 -0500 |
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| b'@@ -1,76 +1,79 @@\n-<tool id="velvetg" name="velvetg" version="@WRAPPER_VERSION@.0">\n+<tool id="velvetg" name="velvetg" version="@WRAPPER_VERSION@.1">\n <description>Velvet sequence assembler for very short reads</description>\n- <version_command>velvetg 2>&1 | grep "Version" | sed -e \'s/Version //\'</version_command>\n <macros>\n <import>macros.xml</import>\n </macros>\n <expand macro="requirements"/>\n <expand macro="stdio"/>\n- <command interpreter="python">\n- velvetg_wrapper.py\n- \'$input.extra_files_path\'\n- #if $generate_amos.afg == "yes":\n- -amos_file $generate_amos.afg\n- #end if\n- #if $unused_reads.generate_unused == "yes":\n- -unused_reads $unused_reads.generate_unused\n- #end if\n- $read_trkg\n- #if $coverage.cutoff == "auto":\n- -cov_cutoff auto\n- #elif $coverage.cutoff == "value":\n- -cov_cutoff $coverage.cov_cutoff\n- #end if\n- #if $expected.coverage == "auto":\n- -exp_cov auto\n- #elif $expected.coverage == "value":\n- -exp_cov $expected.exp_cov\n- #end if\n- #if $contig_lgth.use_contig_lgth == "yes":\n- -min_contig_lgth $contig_lgth.min_contig_lgth\n- #end if\n- #if $reads.paired == "yes":\n- #if int($reads.ins_length) > 0:\n- -ins_length $reads.ins_length\n- #end if\n- #if $reads.options.advanced == "yes":\n- #if int($reads.options.ins_length_sd) > 0:\n- -ins_length_sd $reads.options.ins_length_sd\n- #end if\n- #if int($reads.options.ins_length2) > 0:\n- -ins_length2 $reads.options.ins_length2\n- #end if\n- #if int($reads.options.ins_length2_sd) > 0:\n- -ins_length2_sd $reads.options.ins_length2_sd\n- #end if\n- #if int($reads.options.ins_length_long) > 0:\n- -ins_length_long $reads.options.ins_length_long\n- #end if\n- #if int($reads.options.ins_length_long_sd) > 0:\n- -ins_length_long_sd $reads.options.ins_length_long_sd\n- #end if\n- #if int($reads.options.max_branch_length) > 0:\n- -max_branch_length $reads.options.max_branch_length\n- #end if\n- #if int($reads.options.max_divergence) > 0:\n- -max_divergence $reads.options.max_divergence\n- #end if\n- #if int($reads.options.max_gap_count) > 0:\n- -max_gap_count $reads.options.max_gap_count\n- #end if\n- #if int($reads.options.min_pair_count) > 0:\n- -min_pair_count $reads.options.min_pair_count\n- #end if\n- #if int($reads.options.max_coverage) > 0:\n- -max_coverage $reads.options.max_coverage\n- #end if\n- #if int($reads.options.long_mult_cutoff) > 0:\n- -long_mult_cutoff $reads.options.long_mult_cutoff\n- #end if\n- $reads.options.scaffolding\n- #end if\n- #end if\n- </command>\n+ <version_command><![CDATA[\n+ velvetg 2>&1 | grep "Version" | sed -e \'s/Version //\'\n+ ]]></version_command>\n+ <command><![CDATA[\n+ln -s \'$input.extra_files_path\'/Roadmaps &&\n+ln -s \'$input.extra_files_path\'/Sequences &&\n+velvetg .\n+#if $generate_amos.afg == "yes":\n+ -amos_file $generate_amos.afg\n+#end if\n+#if $unused_reads.generate_unused == "yes":\n+ -unused_reads $unused_reads.generate_unused\n+#end if\n+$read_trkg\n+#if $coverage.cutoff == "auto":\n+ -cov_cutoff auto\n+#elif $coverage.cutoff == "value":\n+ -cov_cutoff $coverage.cov_c'..b'_sd) > 0:\n+ -ins_length_long_sd $reads.options.ins_length_long_sd\n+ #end if\n+ #if int($reads.options.max_branch_length) > 0:\n+ -max_branch_length $reads.options.max_branch_length\n+ #end if\n+ #if int($reads.options.max_divergence) > 0:\n+ -max_divergence $reads.options.max_divergence\n+ #end if\n+ #if int($reads.options.max_gap_count) > 0:\n+ -max_gap_count $reads.options.max_gap_count\n+ #end if\n+ #if int($reads.options.min_pair_count) > 0:\n+ -min_pair_count $reads.options.min_pair_count\n+ #end if\n+ #if int($reads.options.max_coverage) > 0:\n+ -max_coverage $reads.options.max_coverage\n+ #end if\n+ #if int($reads.options.long_mult_cutoff) > 0:\n+ -long_mult_cutoff $reads.options.long_mult_cutoff\n+ #end if\n+ $reads.options.scaffolding\n+ #end if\n+#end if\n+ ]]></command>\n <inputs>\n <param name="input" type="data" format="velvet" label="Velvet Dataset" help="Prepared by velveth."/>\n <conditional name="generate_amos">\n@@ -142,7 +145,7 @@\n <conditional name="reads">\n <param name="paired" type="select" label="Using Paired Reads">\n <option value="no">No</option>\n- <option value="yes" selected="${input.metadata.paired_end_reads}">Yes</option>\n+ <option value="yes">Yes</option>\n </param>\n <when value="no"/>\n <when value="yes">\n@@ -188,15 +191,12 @@\n <data format="tabular" name="stats" label="${tool.name} on ${on_string}: Stats" from_work_dir="stats.txt" />\n <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs" from_work_dir="contigs.fa" />\n </outputs>\n- <requirements>\n- <requirement type="package">velvet</requirement>\n- </requirements>\n <tests>\n <test>\n- <param name="input" value="velveth_test1/output.html" ftype="velvet" >\n- <composite_data value=\'velveth_test1/Sequences\' ftype="Sequences"/>\n- <composite_data value=\'velveth_test1/Roadmaps\' ftype="Roadmaps"/>\n- <composite_data value=\'velveth_test1/Log\'/>\n+ <param name="input" value="velveth_test1/output.html" ftype="velvet">\n+ <composite_data value="velveth_test1/Sequences" />\n+ <composite_data value="velveth_test1/Roadmaps" />\n+ <composite_data value="velveth_test1/Log"/>\n </param>\n <param name="afg" value="yes" />\n <param name="generate_unused" value="yes" />\n@@ -207,15 +207,15 @@\n <param name="use_contig_lgth" value="no" />\n <param name="paired" value="no" />\n <!--\n- <output name="LastGraph" file="velvetg_test1/lastgraph.txt" compare="diff"/>\n+ <output name="LastGraph" file="velvetg_test1/lastgraph.txt"/>\n -->\n- <output name="velvet_asm" file="velvetg_test1/amos.afg" compare="diff"/>\n- <output name="unused_reads_fasta" file="velvetg_test1/unusedreads.fa" compare="diff"/>\n- <output name="stats" file="velvetg_test1/stats.csv" compare="diff"/>\n- <output name="contigs" file="velvetg_test1/contigs.fa" compare="diff"/>\n+ <output name="velvet_asm" file="velvetg_test1/amos.afg" />\n+ <output name="unused_reads_fasta" file="velvetg_test1/unusedreads.fa" />\n+ <output name="stats" file="velvetg_test1/stats.csv" />\n+ <output name="contigs" file="velvetg_test1/contigs.fa" />\n </test>\n </tests>\n- <help>\n+ <help><![CDATA[\n **What it does**\n \n Velvet_ is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom.\n@@ -302,6 +302,6 @@\n directory/LastGraph : special formatted file with all the information on the final graph\n directory/velvet_asm.afg : (if requested) AMOS compatible assembly file\n \n- </help>\n+ ]]></help>\n <expand macro="citation"/>\n </tool>\n' |
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| diff -r 08256557922f -r 5da9a0e2fb2d velvetg_wrapper.py --- a/velvetg_wrapper.py Tue Oct 13 16:38:28 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,46 +0,0 @@ -#!/usr/bin/env python - -""" -Classes encapsulating decypher tool. -James E Johnson - University of Minnesota -""" -import os -import sys -import subprocess - -assert sys.version_info[:2] >= ( 2, 4 ) - -def stop_err( msg ): - sys.stderr.write( "%s\n" % msg ) - sys.exit() - - -def __main__(): - #Parse Command Line - working_dir = sys.argv[1] - inputs = ' '.join(sys.argv[2:]) - for _ in ('Roadmaps', 'Sequences'): - os.symlink(os.path.join(working_dir, _), _) - cmdline = 'velvetg . %s' % (inputs) - print "Command to be executed: %s" % cmdline - try: - proc = subprocess.Popen( args=cmdline, shell=True, stderr=subprocess.PIPE ) - returncode = proc.wait() - # get stderr, allowing for case where it's very large - stderr = '' - buffsize = 1048576 - try: - while True: - stderr += proc.stderr.read( buffsize ) - if not stderr or len( stderr ) % buffsize != 0: - break - except OverflowError: - pass - if returncode != 0: - raise Exception, stderr - except Exception, e: - stop_err( 'Error running velvetg ' + str( e ) ) - - -if __name__ == "__main__": - __main__() |
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| diff -r 08256557922f -r 5da9a0e2fb2d velveth.xml --- a/velveth.xml Tue Oct 13 16:38:28 2015 -0400 +++ b/velveth.xml Wed Feb 12 11:16:32 2020 -0500 |
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| @@ -1,24 +1,27 @@ -<tool id="velveth" name="velveth" version="@WRAPPER_VERSION@.0"> +<tool id="velveth" name="velveth" version="@WRAPPER_VERSION@.1"> <description>Prepare a dataset for the Velvet velvetg Assembler</description> - <version_command>velveth 2>&1 | grep "Version" | sed -e 's/Version //'</version_command> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> - <command interpreter="python"> - velveth_wrapper.py - '$out_file1' '$out_file1.extra_files_path' - $hash_length - $strand_specific - #for $i in $inputs - ${i.file_format} - ${i.read_type} - ${i.input} - #end for - </command> + <version_command><![CDATA[ + velveth 2>&1 | grep "Version" | sed -e 's/Version //' + ]]></version_command> + <command><![CDATA[ +mkdir -p '${out_file1.extra_files_path}' && +velveth +'${out_file1.extra_files_path}' +$hash_length +$strand_specific +#for $i in $inputs + ${i.file_format} + ${i.read_type} + '${i.input}' +#end for + ]]></command> <inputs> - <param label="Hash Length" name="hash_length" type="select" help="k-mer length in base pairs of the words being hashed."> + <param name="hash_length" type="select" label="Hash length" help="k-mer length in base pairs of the words being hashed"> <option value="11">11</option> <option value="13">13</option> <option value="15">15</option> @@ -29,6 +32,87 @@ <option value="25">25</option> <option value="27">27</option> <option value="29">29</option> + <option value="31">31</option> + <option value="33">33</option> + <option value="35">35</option> + <option value="37">37</option> + <option value="39">39</option> + <option value="41">41</option> + <option value="43">43</option> + <option value="45">45</option> + <option value="47">47</option> + <option value="49">49</option> + <option value="51">51</option> + <option value="53">53</option> + <option value="55">55</option> + <option value="57">57</option> + <option value="59">59</option> + <option value="61">61</option> + <option value="63">63</option> + <option value="65">65</option> + <option value="67">67</option> + <option value="69">69</option> + <option value="71">71</option> + <option value="73">73</option> + <option value="75">75</option> + <option value="77">77</option> + <option value="79">79</option> + <option value="81">81</option> + <option value="83">83</option> + <option value="85">85</option> + <option value="87">87</option> + <option value="89">89</option> + <option value="91">91</option> + <option value="93">93</option> + <option value="95">95</option> + <option value="97">97</option> + <option value="99">99</option> + <option value="101">101</option> + <option value="103">103</option> + <option value="105">105</option> + <option value="107">107</option> + <option value="109">109</option> + <option value="111">111</option> + <option value="113">113</option> + <option value="115">115</option> + <option value="117">117</option> + <option value="119">119</option> + <option value="121">121</option> + <option value="123">123</option> + <option value="125">125</option> + <option value="127">127</option> + <option value="129">129</option> + <option value="131">131</option> + <option value="133">133</option> + <option value="135">135</option> + <option value="137">137</option> + <option value="139">139</option> + <option value="141">141</option> + <option value="143">143</option> + <option value="145">145</option> + <option value="147">147</option> + <option value="149">149</option> + <option value="151">151</option> + <option value="153">153</option> + <option value="155">155</option> + <option value="157">157</option> + <option value="159">159</option> + <option value="161">161</option> + <option value="163">163</option> + <option value="165">165</option> + <option value="167">167</option> + <option value="169">169</option> + <option value="171">171</option> + <option value="173">173</option> + <option value="175">175</option> + <option value="177">177</option> + <option value="179">179</option> + <option value="181">181</option> + <option value="183">183</option> + <option value="185">185</option> + <option value="187">187</option> + <option value="189">189</option> + <option value="191">191</option> </param> <param name="strand_specific" type="boolean" checked="false" truevalue="-strand_specific" falsevalue="" label="Use strand specific transcriptome sequencing" help="If you are using a strand specific transcriptome sequencing protocol, you may wish to use this option for better results."/> <repeat name="inputs" title="Input Files"> @@ -51,11 +135,8 @@ </repeat> </inputs> <outputs> - <data format="velvet" name="out_file1" /> + <data name="out_file1" format="velvet" /> </outputs> - <requirements> - <requirement type="package">velvet</requirement> - </requirements> <tests> <test> <param name="hash_length" value="21" /> @@ -67,13 +148,12 @@ <!-- </repeat> --> <param name="strand_specific" value="" /> <output name="out_file1" file="velveth_test1/output.html" lines_diff="4"> - <extra_files type="file" name='Sequences' value="velveth_test1/Sequences" compare="diff" /> - <extra_files type="file" name='Roadmaps' value="velveth_test1/Roadmaps" compare="diff" /> + <extra_files type="file" name="Sequences" value="velveth_test1/Sequences" /> + <extra_files type="file" name="Roadmaps" value="velveth_test1/Roadmaps" /> </output> </test> </tests> - <help> - + <help><![CDATA[ **What it does** Velvet_ is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom. @@ -130,7 +210,6 @@ shortPaired2 (see above) long (for Sanger, 454 or even reference sequences) longPaired - - </help> + ]]></help> <expand macro="citation"/> </tool> |
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| diff -r 08256557922f -r 5da9a0e2fb2d velveth_wrapper.py --- a/velveth_wrapper.py Tue Oct 13 16:38:28 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,65 +0,0 @@ -#!/usr/bin/env python - -""" -Classes encapsulating decypher tool. -James E Johnson - University of Minnesota -""" -import pkg_resources -import logging, os, string, sys, tempfile, glob, shutil, types, urllib -import shlex, subprocess -from optparse import OptionParser, OptionGroup -from stat import * - - -log = logging.getLogger( __name__ ) - -assert sys.version_info[:2] >= ( 2, 4 ) - -def stop_err( msg ): - sys.stderr.write( "%s\n" % msg ) - sys.exit() - -def __main__(): - #Parse Command Line - s = 'velveth_wrapper.py: argv = %s\n' % (sys.argv) - argcnt = len(sys.argv) - html_file = sys.argv[1] - working_dir = sys.argv[2] - try: # for test - needs this done - os.makedirs(working_dir) - except Exception, e: - stop_err( 'Error running velveth ' + str( e ) ) - hash_length = sys.argv[3] - inputs = string.join(sys.argv[4:],' ') - cmdline = 'velveth %s %s %s > /dev/null' % (working_dir, hash_length, inputs) - try: - proc = subprocess.Popen( args=cmdline, shell=True, stderr=subprocess.PIPE ) - returncode = proc.wait() - # get stderr, allowing for case where it's very large - stderr = '' - buffsize = 1048576 - try: - while True: - stderr += proc.stderr.read( buffsize ) - if not stderr or len( stderr ) % buffsize != 0: - break - except OverflowError: - pass - if returncode != 0: - raise Exception, stderr - except Exception, e: - stop_err( 'Error running velveth ' + str( e ) ) - sequences_path = os.path.join(working_dir,'Sequences') - roadmaps_path = os.path.join(working_dir,'Roadmaps') - rval = ['<html><head><title>Velvet Galaxy Composite Dataset </title></head><p/>'] - rval.append('<div>%s<p/></div>' % (cmdline) ) - rval.append('<div>This composite dataset is composed of the following files:<p/><ul>') - rval.append( '<li><a href="%s" type="text/plain">%s </a>%s</li>' % (sequences_path,'Sequences','Sequences' ) ) - rval.append( '<li><a href="%s" type="text/plain">%s </a>%s</li>' % (roadmaps_path,'Roadmaps','Roadmaps' ) ) - rval.append( '</ul></div></html>' ) - f = file(html_file,'w') - f.write("\n".join( rval )) - f.write('\n') - f.close() - -if __name__ == "__main__": __main__() |